Merge remote-tracking branch 'origin/master' into core-updates

 Conflicts:
	doc/guix.texi
	gnu/local.mk
	gnu/packages/admin.scm
	gnu/packages/base.scm
	gnu/packages/chromium.scm
	gnu/packages/compression.scm
	gnu/packages/databases.scm
	gnu/packages/diffoscope.scm
	gnu/packages/freedesktop.scm
	gnu/packages/gnome.scm
	gnu/packages/gnupg.scm
	gnu/packages/guile.scm
	gnu/packages/inkscape.scm
	gnu/packages/llvm.scm
	gnu/packages/openldap.scm
	gnu/packages/pciutils.scm
	gnu/packages/ruby.scm
	gnu/packages/samba.scm
	gnu/packages/sqlite.scm
	gnu/packages/statistics.scm
	gnu/packages/syndication.scm
	gnu/packages/tex.scm
	gnu/packages/tls.scm
	gnu/packages/version-control.scm
	gnu/packages/xml.scm
	guix/build-system/copy.scm
	guix/scripts/home.scm

1 files changed, 3087 insertions, 856 deletions

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 10b70bab06..711b988e7f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1,17 +1,18 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015-2023 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016, 2017, 2018, 2020, 2021 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
 ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
 ;;; Copyright © 2017, 2022 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2017, 2018, 2019, 2020, 2021 Tobias Geerinckx-Rice <me@tobias.gr>
-;;; Copyright © 2019, 2020, 2021, 2022 Simon Tournier <zimon.toutoune@gmail.com>
+;;; Copyright © 2019, 2020, 2021, 2022, 2023 Simon Tournier <zimon.toutoune@gmail.com>
 ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
-;;; Copyright © 2020, 2021, 2022 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
+;;; Copyright © 2020-2023 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
 ;;; Copyright © 2021 Hong Li <hli@mdc-berlin.de>
 ;;; Copyright © 2021 Tim Howes <timhowes@lavabit.com>
 ;;; Copyright © 2021 Nicolas Vallet <nls.vallet@gmail.com>
+;;; Copyright © 2023 Navid Afkhami <Navid.Afkhami@mdc-berlin.de>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -48,6 +49,7 @@
   #:use-module (gnu packages graphviz)
   #:use-module (gnu packages haskell-xyz)
   #:use-module (gnu packages image)
+  #:use-module (gnu packages java)
   #:use-module (gnu packages maths)
   #:use-module (gnu packages netpbm)
   #:use-module (gnu packages python)
@@ -505,6 +507,31 @@ ID and species.  It is used by functions in the GenomeInfoDb package.")
 information about the latest version of the Gene Ontologies.")
     (license license:artistic2.0)))
 
+(define-public r-hdo-db
+  (package
+    (name "r-hdo-db")
+    (version "0.99.1")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "HDO.db" version 'annotation))
+              (sha256
+               (base32
+                "14ngyxailmxrbxqqi9m7mchqcvchmbg7zm34i8a927b20s6z4z61"))))
+    (properties `((upstream-name . "HDO.db")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-annotationdbi))
+    (native-inputs
+     (list r-knitr))
+    (home-page "https://bioconductor.org/packages/HDO.db")
+    (synopsis "Annotation maps describing the entire Human Disease Ontology")
+    (description
+     "This package provides a set of annotation maps describing the entire
+Human Disease Ontology.  The annotation data comes from
+@url{Humam Disease Ontology repository,
+https://github.com/DiseaseOntology/HumanDiseaseOntology/tree/main/src/ontology}.")
+    (license license:artistic2.0)))
+
 (define-public r-homo-sapiens
   (package
     (name "r-homo-sapiens")
@@ -1265,6 +1292,26 @@ from Illumina 450k methylation arrays.")
 biscuiteer.")
     (license license:gpl3)))
 
+(define-public r-breakpointrdata
+  (package
+    (name "r-breakpointrdata")
+    (version "1.16.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "breakpointRdata" version 'experiment))
+              (sha256
+               (base32
+                "0f23i4ynb4vgn22c3d2l64z92rzv3qnwd4j8qyvalklrxkwilhfn"))))
+    (properties `((upstream-name . "breakpointRdata")))
+    (build-system r-build-system)
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/daewoooo/breakpointRdata")
+    (synopsis "Strand-seq data for demonstration purposes")
+    (description
+     "This package is a collection of Strand-seq data.  The main purpose is to
+demonstrate functionalities of the @code{breakpointR} package.")
+    (license license:expat)))
+
 (define-public r-celldex
   (package
     (name "r-celldex")
@@ -1384,6 +1431,29 @@ genomation package.  Included are Chip Seq, Methylation and Cage data,
 downloaded from Encode.")
     (license license:gpl3+)))
 
+(define-public r-macrophage
+  (package
+    (name "r-macrophage")
+    (version "1.12.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "macrophage" version
+                                     'experiment))
+              (sha256
+               (base32
+                "0ml8v92w021fmzsn4yl90ap3l4l3b9c1pk8pzsrm122p82wzlyms"))))
+    (properties `((upstream-name . "macrophage")))
+    (build-system r-build-system)
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/macrophage")
+    (synopsis "Human macrophage immune response data")
+    (description
+     "This package provides the output of running @code{Salmon} on a set of 24
+RNA-seq samples from Alasoo, et al. \"Shared genetic effects on chromatin and
+gene expression indicate a role for enhancer priming in immune response\", published
+in Nature Genetics, January 2018.")
+    (license license:gpl2+)))
+
 (define-public r-msdata
   (package
     (name "r-msdata")
@@ -1605,19 +1675,43 @@ cultures from 4 patients at 2 time points over 3 conditions (DPN, OHT and contro
 TCGAbiolinksGUI package.")
     (license license:gpl3)))
 
+(define-public r-tximportdata
+  (package
+    (name "r-tximportdata")
+    (version "1.24.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "tximportData" version
+                                     'experiment))
+              (sha256
+               (base32
+                "0mgbwpybg2xd6x1ijrflmjh5w63qz6ylnzszbbyp437n618m7riy"))))
+    (properties `((upstream-name . "tximportData")))
+    (build-system r-build-system)
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/tximportData")
+    (synopsis "Data for the tximport package")
+    (description
+     "This package provides the output of running various transcript abundance
+quantifiers on a set of 6 RNA-seq samples from the GEUVADIS project.  The
+quantifiers were @code{Cufflinks}, @code{RSEM}, @code{kallisto}, @code{Salmon}
+and @code{Sailfish}.  Alevin example output is also included.")
+    (license license:gpl2+)))
+
+
 
 ;;; Packages
 
 (define-public r-abarray
   (package
     (name "r-abarray")
-    (version "1.64.0")
+    (version "1.66.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "ABarray" version))
               (sha256
                (base32
-                "0kjq00i2mb21xyjjs3jy09ps80f11cy37wywzjvmxyjxzbsk4d7r"))))
+                "02rjxzbrzphl28z8zpgw3gavzlzlx71n5ld8sb3im6xpn81ykvfh"))))
     (properties `((upstream-name . "ABarray")))
     (build-system r-build-system)
     (propagated-inputs (list r-biobase r-multtest))
@@ -1637,13 +1731,13 @@ into folders according to the analysis settings used.")
 (define-public r-absseq
   (package
     (name "r-absseq")
-    (version "1.50.0")
+    (version "1.52.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "ABSSeq" version))
               (sha256
                (base32
-                "1kwl0gcqwbgblwvpbvqlgnsi91km77j11f0q1f0gd6hhnv38mmlv"))))
+                "1ypd0wg3k2zzl0zf15c16dc38hfpsm5vv4x0x0yf90x0f8b6jpaz"))))
     (properties `((upstream-name . "ABSSeq")))
     (build-system r-build-system)
     (propagated-inputs (list r-limma r-locfit))
@@ -1666,13 +1760,13 @@ ranking by fold-change and visualization.")
 (define-public r-adam
   (package
     (name "r-adam")
-    (version "1.12.0")
+    (version "1.14.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "ADAM" version))
               (sha256
                (base32
-                "1cgcjykik9hjrwlvvgaccprcrimgq5kwh9cj6367yk9m574a4gmn"))))
+                "1s1mzjxqld8gllfh6z9kg30klb4y1jrkrif7vwr18c0mhamf47a6"))))
     (properties `((upstream-name . "ADAM")))
     (build-system r-build-system)
     (propagated-inputs (list r-dplyr
@@ -1701,13 +1795,13 @@ functionally associated genes} (GFAG).")
 (define-public r-adamgui
   (package
     (name "r-adamgui")
-    (version "1.12.0")
+    (version "1.14.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "ADAMgui" version))
               (sha256
                (base32
-                "0vvd5qdwkfcr7zg7z63x3vvrcg63r6c9p383yvcg2lp8zmx8hsbs"))))
+                "1ks799kgdmlxn5iyj6rzj04cm28klivclz3bg6bc4wad2q7h4ra9"))))
     (properties `((upstream-name . "ADAMgui")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1749,13 +1843,13 @@ the @code{GFAGpathUi} function.")
 (define-public r-adimpute
   (package
     (name "r-adimpute")
-    (version "1.6.0")
+    (version "1.8.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "ADImpute" version))
               (sha256
                (base32
-                "0885kd8mpmwjpzpx14pi6l3mqcvsixk10vkf5h4sqb7di0nnna4w"))))
+                "0wrprxd91vi4wwh9wixhx1ppbjsb56r4kcxgqz8w6ahr3z2387im"))))
     (properties `((upstream-name . "ADImpute")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1798,13 +1892,13 @@ results from different methods into an ensemble.")
 (define-public r-adsplit
   (package
     (name "r-adsplit")
-    (version "1.66.0")
+    (version "1.68.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "adSplit" version))
               (sha256
                (base32
-                "1wl2gd0b7krf485clw67cxayp0g9argklkzn8nw1vrkil0vvr4jm"))))
+                "0a05j1g42wnw5lcn6g6vp2z3mnjz185b2hvdg362ln270r19gch6"))))
     (properties `((upstream-name . "adSplit")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1826,13 +1920,13 @@ the supporting gene set is determined.")
 (define-public r-affixcan
   (package
     (name "r-affixcan")
-    (version "1.14.0")
+    (version "1.16.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AffiXcan" version))
               (sha256
                (base32
-                "0wj9shzmlxpksbxny571xzfcmmqqzjlk1vq4mx1is2r6ma7jkblq"))))
+                "1jsdl477qhsq3rpqvgdm7navr4izpppfkiw0fvlhxwspgp3fjs6c"))))
     (properties `((upstream-name . "AffiXcan")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1854,13 +1948,13 @@ expression values are known.")
 (define-public r-affyrnadegradation
   (package
     (name "r-affyrnadegradation")
-    (version "1.42.0")
+    (version "1.44.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AffyRNADegradation" version))
               (sha256
                (base32
-                "16akwmpzwxai7ks5bvc1yyb9sx2scv9b9gas5avb0sk5fk0h3nsf"))))
+                "1n6x2c0h6xmcll7mxq4n1y8ahqfmba8ppdcrjk9hf3nh5wngprkz"))))
     (properties `((upstream-name . "AffyRNADegradation")))
     (build-system r-build-system)
     (propagated-inputs (list r-affy))
@@ -1879,13 +1973,13 @@ of samples that are affected by RNA degradation.")
 (define-public r-agdex
   (package
     (name "r-agdex")
-    (version "1.44.0")
+    (version "1.46.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AGDEX" version))
               (sha256
                (base32
-                "0c44fw5ajdjc13409rn3lsv0jhlqa2qcak9b1k8hpig486xxzsr9"))))
+                "0yvdx32yr4mv7dl5ycpbxhrkm6csrr7k3398ggjavdcfhz54dgr8"))))
     (properties `((upstream-name . "AGDEX")))
     (build-system r-build-system)
     (propagated-inputs (list r-biobase r-gseabase))
@@ -1906,13 +2000,13 @@ experiment.")
 (define-public r-aggregatebiovar
   (package
     (name "r-aggregatebiovar")
-    (version "1.6.0")
+    (version "1.8.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "aggregateBioVar" version))
               (sha256
                (base32
-                "0ngg12bgr95m4wm12scmrb55dgy4909c6qrg169l6dkng99v4nx1"))))
+                "1snsc2430cc7cd0k01n1rwa6vympd79g1mcch0paxxkq7msvfn42"))))
     (properties `((upstream-name . "aggregateBioVar")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1940,13 +2034,13 @@ bulk RNA-seq tools.")
 (define-public r-agilp
   (package
     (name "r-agilp")
-    (version "3.28.0")
+    (version "3.30.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "agilp" version))
               (sha256
                (base32
-                "1pm329y2nfcnx98ggxq0prdd5pxfcl5iylvsjjnhw5lyz1awg1yf"))))
+                "15cw004g1vxfwvf939018vmlv9gym4r473jissamkygqdv78hcr0"))))
     (properties `((upstream-name . "agilp")))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/agilp")
@@ -1962,13 +2056,13 @@ but which also provides utilities which may be useful for other platforms.")
 (define-public r-adductomicsr
   (package
     (name "r-adductomicsr")
-    (version "1.12.0")
+    (version "1.14.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "adductomicsR" version))
               (sha256
                (base32
-                "0623qf06xgdsyz0in2wnxwvpdw8kj6cnwf8vlqmgp7g0n3w701ys"))))
+                "0h180k4r1lrij1smpibbqgiki1hb2q87n5ay6habig4bxzbx773x"))))
     (properties `((upstream-name . "adductomicsR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2007,13 +2101,13 @@ mass spectrometry} (MS1) data.")
 (define-public r-agimicrorna
   (package
     (name "r-agimicrorna")
-    (version "2.46.0")
+    (version "2.48.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AgiMicroRna" version))
               (sha256
                (base32
-                "0jic89gyphbv7jzlfgm9bh1aq48lp86rq6hr34gsg9z0pa1192xa"))))
+                "0q3hynyd4dhhh1a2b27y3rrshgvxfwv17k7yabh6g4pc12c33mf7"))))
     (properties `((upstream-name . "AgiMicroRna")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2034,16 +2128,87 @@ using the linear model features implemented in limma.  Standard Bioconductor
 objects are used so that other packages could be used as well.")
     (license license:gpl3)))
 
+(define-public r-aims
+  (package
+    (name "r-aims")
+    (version "1.30.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "AIMS" version))
+              (sha256
+               (base32
+                "1civ4a14ynccv6xs27fm95fw6254l1z0q37546ivyv2mhbz0d2i1"))))
+    (properties `((upstream-name . "AIMS")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-biobase r-e1071))
+    (home-page "https://git.bioconductor.org/packages/AIMS")
+    (synopsis
+     "Absolute assignment of breast cancer intrinsic molecular subtype")
+    (description
+     "This package contains an implementation of @code{AIMS} -- Absolute
+Intrinsic Molecular Subtyping.  It contains necessary functions to assign the
+five intrinsic molecular subtypes (Luminal A, Luminal B, Her2-enriched,
+Basal-like, Normal-like).  Assignments could be done on individual samples as
+well as on dataset of gene expression data.")
+    (license license:artistic2.0)))
+
+(define-public r-airpart
+  (package
+    (name "r-airpart")
+    (version "1.6.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "airpart" version))
+              (sha256
+               (base32
+                "07zxv0sjhlajaw4gxpjni14qyyqn70ar8ph5cpibzcky1lx6pmkl"))))
+    (properties `((upstream-name . "airpart")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-apeglm
+           r-clue
+           r-complexheatmap
+           r-dplyr
+           r-dynamictreecut
+           r-emdbook
+           r-forestplot
+           r-ggplot2
+           r-lpsolve
+           r-matrixstats
+           r-mclust
+           r-pbapply
+           r-plyr
+           r-rcolorbrewer
+           r-rlang
+           r-s4vectors
+           r-scater
+           r-singlecellexperiment
+           r-smurf
+           r-summarizedexperiment))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/airpart")
+    (synopsis "Differential cell-type-specific allelic imbalance")
+    (description
+     "The airpart package identifies sets of genes displaying differential
+cell-type-specific allelic imbalance across cell types or states, utilizing
+single-cell allelic counts.  It makes use of a generalized fused lasso with
+binomial observations of allelic counts to partition cell types by their
+allelic imbalance.  Alternatively, a nonparametric method for partitioning
+cell types is offered.  The package includes a number of visualizations and
+quality control functions for examining single cell allelic imbalance
+datasets.")
+    (license license:gpl2)))
+
 (define-public r-amountain
   (package
     (name "r-amountain")
-    (version "1.22.0")
+    (version "1.24.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AMOUNTAIN" version))
               (sha256
                (base32
-                "0vdfabsrisdd7qq28f5ivd0v8zz49szqn677i5lhwnlaix220c54"))))
+                "0zzl5dv64yhdivsm2pgsfjikygib9pkfiv34h1lnmqrj6yivvvw8"))))
     (properties `((upstream-name . "AMOUNTAIN")))
     (build-system r-build-system)
     (inputs (list gsl))
@@ -2058,16 +2223,63 @@ conditions or various species.  @code{AMOUNTAIN} aims to search active modules
 in multi-layer WGCN using a continuous optimization approach.")
     (license license:gpl2+)))
 
+(define-public r-amplican
+  (package
+    (name "r-amplican")
+    (version "1.20.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "amplican" version))
+              (sha256
+               (base32
+                "1c990i6gxbarcpbdpkz017x94spwzap95l95synlizbkyif4z8ij"))))
+    (properties `((upstream-name . "amplican")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biocgenerics
+           r-biocparallel
+           r-biostrings
+           r-clustercrit
+           r-data-table
+           r-dplyr
+           r-genomeinfodb
+           r-genomicranges
+           r-ggplot2
+           r-ggthemes
+           r-gridextra
+           r-gtable
+           r-iranges
+           r-knitr
+           r-matrix
+           r-matrixstats
+           r-rcpp
+           r-rmarkdown
+           r-s4vectors
+           r-shortread
+           r-stringr
+           r-waffle))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/valenlab/amplican")
+    (synopsis "Automated analysis of CRISPR experiments")
+    (description
+     "The package performs alignment of the amplicon reads, normalizes
+gathered data, calculates multiple statistics (e.g. cut rates, frameshifts)
+and presents the results in the form of aggregated reports.  Data and
+statistics can be broken down by experiments, barcodes, user defined groups,
+guides and amplicons allowing for quick identification of potential
+problems.")
+    (license license:gpl3)))
+
 (define-public r-amaretto
   (package
     (name "r-amaretto")
-    (version "1.12.0")
+    (version "1.13.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AMARETTO" version))
               (sha256
                (base32
-                "111dk19b9910icksyr592cvhc5gwvgknr5q4887j9yxbajd7hcmx"))))
+                "18w65sf3h4yzw9v5xgkalxnkmgzgsx100v7qc7z4ifx10lgpji5n"))))
     (properties `((upstream-name . "AMARETTO")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2113,13 +2325,13 @@ canonical cancer pathways.")
 (define-public r-anaquin
   (package
     (name "r-anaquin")
-    (version "2.20.0")
+    (version "2.22.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Anaquin" version))
               (sha256
                (base32
-                "1jgpnls2djl1yzvnk64qc83mljmlci7wflwkza3wr0sv6r47b0dd"))))
+                "08y2syaacy15rxcf3x2r3906kfm58fkx7ainaqvy5inlc9f670j5"))))
     (properties `((upstream-name . "Anaquin")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2140,16 +2352,408 @@ of Medical Research.  The goal is to provide a standard library for quantitative
 analysis, modelling, and visualization of spike-in controls.")
     (license license:bsd-3)))
 
+(define-public r-ancombc
+  (package
+    (name "r-ancombc")
+    (version "2.0.2")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "ANCOMBC" version))
+              (sha256
+               (base32
+                "0dlinv4vhxgni8ygzvfw8pbc6d1v9x5chhrpxblhs2c65bkgyxz5"))))
+    (properties `((upstream-name . "ANCOMBC")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-cvxr
+           r-desctools
+           r-doparallel
+           r-dorng
+           r-dplyr
+           r-emmeans
+           r-energy
+           r-foreach
+           r-hmisc
+           r-lme4
+           r-lmertest
+           r-magrittr
+           r-mass
+           r-mia
+           r-nloptr
+           r-rdpack
+           r-rlang
+           r-rngtools
+           r-s4vectors
+           r-singlecellexperiment
+           r-summarizedexperiment
+           r-tibble
+           r-tidyr
+           r-treesummarizedexperiment))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/FrederickHuangLin/ANCOMBC")
+    (synopsis "Analysis of compositions of microbiomes with bias correction")
+    (description
+     "@code{ANCOMBC} is a package containing @dfn{differential abundance} (DA)
+and correlation analyses for microbiome data.  Specifically, the package
+includes @dfn{Analysis of Compositions of Microbiomes with Bias
+Correction}(ANCOM-BC) and @dfn{Analysis of Composition of Microbiomes} (ANCOM)
+for DA analysis, and @dfn{Sparse Estimation of Correlations among
+Microbiomes} (SECOM) for correlation analysis.  Microbiome data are typically
+subject to two sources of biases: unequal sampling fractions (sample-specific
+biases) and differential sequencing efficiencies (taxon-specific biases).
+Methodologies included in the @code{ANCOMBC} package were designed to correct
+these biases and construct statistically consistent estimators.")
+    (license license:artistic2.0)))
+
+(define-public r-animalcules
+  (package
+    (name "r-animalcules")
+    (version "1.14.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "animalcules" version))
+              (sha256
+               (base32
+                "1alpsamrglgvzhcibkaf7m3gyiv61wbj1gvsq4lw6vjka100j9qr"))))
+    (properties `((upstream-name . "animalcules")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-ape
+           r-assertthat
+           r-biomformat
+           r-caret
+           r-covr
+           r-deseq2
+           r-dplyr
+           r-dt
+           r-forcats
+           r-ggplot2
+           r-glmnet
+           r-gunifrac
+           r-lattice
+           r-limma
+           r-magrittr
+           r-matrix
+           r-multiassayexperiment
+           r-plotly
+           r-plotroc
+           r-rentrez
+           r-reshape2
+           r-s4vectors
+           r-scales
+           r-shiny
+           r-shinyjs
+           r-summarizedexperiment
+           r-tibble
+           r-tsne
+           r-umap
+           r-vegan
+           r-xml))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/compbiomed/animalcules")
+    (synopsis "Interactive microbiome analysis toolkit")
+    (description
+     "Animalcules is an R package for utilizing up-to-date data analytics,
+visualization methods, and machine learning models to provide users an
+easy-to-use interactive microbiome analysis framework.  It can be used as a
+standalone software package or users can explore their data with the
+accompanying interactive R Shiny application.  Traditional microbiome analysis
+such as alpha/beta diversity and differential abundance analysis are enhanced,
+while new methods like biomarker identification are introduced by animalcules.
+Powerful interactive and dynamic figures generated by animalcules enable users
+to understand their data better and discover new insights.")
+    (license license:artistic2.0)))
+
+(define-public r-anvil
+  (package
+    (name "r-anvil")
+    (version "1.10.1")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "AnVIL" version))
+              (sha256
+               (base32
+                "0iqsffkrxv28g9cddx2w05f2dbscwxhh6bpizwa8xaxhvn5bcpsv"))))
+    (properties `((upstream-name . "AnVIL")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biocmanager
+           r-dplyr
+           r-dt
+           r-futile-logger
+           r-htmltools
+           r-httr
+           r-jsonlite
+           r-miniui
+           r-rapiclient
+           r-rlang
+           r-shiny
+           r-tibble
+           r-tidyr
+           r-tidyselect))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/AnVIL")
+    (synopsis "Provides access to AnVIL, Terra, Leonardo and other projects")
+    (description
+     "The AnVIL is a cloud computing resource developed in part by the
+National Human Genome Research Institute.  The AnVIL package provides end-user
+and developer functionality.  AnVIL provides fast binary package installation,
+utilities for working with Terra/AnVIL table and data resources, and
+convenient functions for file movement to and from Google cloud storage.  For
+developers, AnVIL provides programatic access to the Terra, Leonardo, Rawls,
+Dockstore, and Gen3 RESTful programming interface, including helper functions
+to transform JSON responses to formats more amenable to manipulation in R.")
+    (license license:artistic2.0)))
+
+(define-public r-aldex2
+  (package
+    (name "r-aldex2")
+    (version "1.30.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "ALDEx2" version))
+              (sha256
+               (base32
+                "0585s5pb8zr9il1vhxw9vjzzajmdcjmf9zz3zlc5vpczd3fnzfkf"))))
+    (properties `((upstream-name . "ALDEx2")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biocparallel
+           r-genomicranges
+           r-iranges
+           r-multtest
+           r-rfast
+           r-s4vectors
+           r-summarizedexperiment
+           r-zcompositions))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/ggloor/ALDEx_bioc")
+    (synopsis "Analysis of differential abundance taking sample variation into account")
+    (description
+     "This package provides a differential abundance analysis for the
+comparison of two or more conditions.  Useful for analyzing data from standard
+RNA-seq or meta-RNA-seq assays as well as selected and unselected values from
+in-vitro sequence selections.  Uses a Dirichlet-multinomial model to infer
+abundance from counts, optimized for three or more experimental replicates.
+The method infers biological and sampling variation to calculate the expected
+false discovery rate, given the variation, based on a Wilcoxon Rank Sum test
+and Welch's t-test, a Kruskal-Wallis test, a generalized linear model, or a
+correlation test.  All tests report p-values and Benjamini-Hochberg corrected
+p-values.  ALDEx2 also calculates expected standardized effect sizes for
+paired or unpaired study designs.")
+    ;; The code for the function "rdirichlet" is from the R package
+    ;; "mc2d_0.1-14.tar.gz", which is denoted as GPL>=2, and where the
+    ;; package's LICENSE is specified as GPL-3.
+    (license (list license:agpl3+ license:gpl2+ license:gpl3))))
+
+(define-public r-alevinqc
+  (package
+    (name "r-alevinqc")
+    (version "1.14.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "alevinQC" version))
+              (sha256
+               (base32
+                "0rd64j4hkdk2d6mlld6qkv2m96lqc93807xjdf05xm8qkyx8g8y2"))))
+    (properties `((upstream-name . "alevinQC")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-cowplot
+           r-dplyr
+           r-dt
+           r-ggally
+           r-ggplot2
+           r-rcpp
+           r-rjson
+           r-rlang
+           r-rmarkdown
+           r-shiny
+           r-shinydashboard
+           r-tximport))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/csoneson/alevinQC")
+    (synopsis "Quality control reports for @code{Alevin} output")
+    (description
+     "The package @code{r-alevinqc} generates quality control reports
+summarizing the output from an @code{alevin} run.  The reports can be
+generated as HTML or PDF files, or as Shiny applications.")
+    (license license:expat)))
+
+(define-public r-alphabeta
+  (package
+    (name "r-alphabeta")
+    (version "1.12.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "AlphaBeta" version))
+              (sha256
+               (base32
+                "000apg879li9wkbyrl8cm73z6h0xasqp41h9ir9hywy2v38rmc5b"))))
+    (properties `((upstream-name . "AlphaBeta")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biocparallel
+           r-data-table
+           r-dplyr
+           r-expm
+           r-ggplot2
+           r-gtools
+           r-igraph
+           r-optimx
+           r-plotly
+           r-stringr))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/AlphaBeta")
+    (synopsis "Estimate epimutation rates and spectra from DNA methylations in plants")
+    (description
+     "The package @code{AlphaBeta} is a computational method for estimating
+epimutation rates and spectra from high-throughput DNA methylation data in
+plants.  The method has been specifically designed to:
+
+@itemize
+@item analyze @emph{germline} epimutations in the context of
+  multi-generational mutation accumulation lines;
+@item analyze @emph{somatic} epimutations in the context of plant development
+  and aging.
+@end itemize")
+    (license license:gpl3)))
+
+(define-public r-alpine
+  (package
+    (name "r-alpine")
+    (version "1.24.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "alpine" version))
+              (sha256
+               (base32
+                "0rjnwljh4c2f7ml0m14pllns4pvyjwwf23qsn6zjygm5x04bapf0"))))
+    (properties `((upstream-name . "alpine")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biostrings
+           r-genomeinfodb
+           r-genomicalignments
+           r-genomicfeatures
+           r-genomicranges
+           r-graph
+           r-iranges
+           r-rbgl
+           r-rsamtools
+           r-s4vectors
+           r-speedglm
+           r-stringr
+           r-summarizedexperiment))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/alpine")
+    (synopsis "Modeling and correcting fragment sequence bias")
+    (description
+     "The package @code{alpine} helps to model bias parameters and then using
+those parameters to estimate RNA-seq transcript abundance.  @code{Alpine} is a
+package for estimating and visualizing many forms of sample-specific biases that
+can arise in RNA-seq, including fragment length distribution, positional bias on
+the transcript, read start bias (random hexamer priming), and fragment GC-content
+(amplification).  It also offers bias-corrected estimates of transcript
+abundance in @dfn{FPKM}(Fragments Per Kilobase of transcript per Million
+mapped reads).  It is currently designed for un-stranded paired-end RNA-seq
+data.")
+    (license license:gpl2+)))
+
+(define-public r-alpsnmr
+  (package
+    (name "r-alpsnmr")
+    (version "4.0.2")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "AlpsNMR" version))
+              (sha256
+               (base32
+                "1y4qqc6l8flv5ns4qwzjwmcykm6zcm4jg097mn8xyp7mnxymy7pl"))))
+    (properties `((upstream-name . "AlpsNMR")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-baseline
+           r-biocparallel
+           r-dplyr
+           r-fs
+           r-future
+           r-generics
+           r-ggplot2
+           r-glue
+           r-htmltools
+           r-magrittr
+           r-matrixstats
+           r-mixomics
+           r-pcapp
+           r-purrr
+           r-readxl
+           r-reshape2
+           r-rlang
+           r-rmarkdown
+           r-scales
+           r-signal
+           r-speaq
+           r-stringr
+           r-tibble
+           r-tidyr
+           r-tidyselect
+           r-vctrs))
+    (native-inputs (list r-knitr))
+    (home-page "https://sipss.github.io/AlpsNMR/")
+    (synopsis "Automated spectral processing system for NMR")
+    (description
+     "This package reads Bruker @acronym{NMR, Nuclear Magnetic Resonance} data
+directories both zipped and unzipped.  It provides automated and efficient
+signal processing for untargeted NMR metabolomics.  It is able to interpolate
+the samples, detect outliers, exclude regions, normalize, detect peaks, align
+the spectra, integrate peaks, manage metadata and visualize the spectra.
+After spectra processing, it can apply multivariate analysis on extracted
+data.  Efficient plotting with 1-D data is also available.  Basic reading of
+1D ACD/Labs exported JDX samples is also available.")
+    (license license:expat)))
+
+(define-public r-altcdfenvs
+  (package
+    (name "r-altcdfenvs")
+    (version "2.60.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "altcdfenvs" version))
+              (sha256
+               (base32
+                "0fm4l93j6nm1w1w57zzryc1hkzapp8l16pkwjzdzllvwvsnsg8r0"))))
+    (properties `((upstream-name . "altcdfenvs")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-affy
+           r-biobase
+           r-biocgenerics
+           r-biostrings
+           r-hypergraph
+           r-makecdfenv
+           r-s4vectors))
+    (home-page "https://bioconductor.org/packages/altcdfenvs")
+    (synopsis
+     "Convenience data structures and functions to handle CDF environments")
+    (description
+     "The package is usable with Affymetrix GeneChip short oligonucleotide
+arrays, and it can be adapted or extended to other platforms.  It is able to
+modify or replace the grouping of probes in the probe sets.  Also, the package
+contains simple functions to read R connections in the FASTA format and it can
+create an alternative mapping from sequences.")
+    (license license:gpl2+)))
+
 (define-public r-aneufinder
   (package
     (name "r-aneufinder")
-    (version "1.24.0")
+    (version "1.26.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AneuFinder" version))
               (sha256
                (base32
-                "1acsp987jv2x4qwbgy3y7ff4r2qz7680b0nbr37m4lmncqfgh8yl"))))
+                "154cg63n7h9h5jkj00aqf0hzbmmjg16bzvvk50fyixwq0a4q1j00"))))
     (build-system r-build-system)
     (native-inputs
      (list r-knitr))
@@ -2185,13 +2789,13 @@ sequencing data.")
 (define-public r-anf
   (package
     (name "r-anf")
-    (version "1.18.0")
+    (version "1.20.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "ANF" version))
               (sha256
                (base32
-                "1fa2pbdapymrpz01ws0m2fbzf11d723x6rbsys29v06is57f5lpj"))))
+                "0yfwvgx7144r894fr13sx4gyyq6ljh7y734wx74sb7q80cl2gs1j"))))
     (properties `((upstream-name . "ANF")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2213,13 +2817,13 @@ network fusion.")
 (define-public r-annmap
   (package
     (name "r-annmap")
-    (version "1.38.0")
+    (version "1.40.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "annmap" version))
               (sha256
                (base32
-                "0ywqbb8jia7rrkzcsf6a11kqf8dnx96z8n8xw7067mahycykbixv"))))
+                "18ia189qgsbcivpfsfss05dnd3kdc6gmswq8i1whwf9n227b2cv3"))))
     (properties `((upstream-name . "annmap")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2247,13 +2851,13 @@ Functions to plot gene architecture and BAM file data are also provided.")
 (define-public r-antiprofiles
   (package
     (name "r-antiprofiles")
-    (version "1.36.0")
+    (version "1.38.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "antiProfiles" version))
               (sha256
                (base32
-                "1277kg5xpyb2yriyjy18p437q5lj22h4al7z7pygkzxzywxv9g40"))))
+                "0f32373ncfjbvy05yngmfhhdgyc99a4idz3ry2xlabdmrbs5yac3"))))
     (properties `((upstream-name . "antiProfiles")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2270,17 +2874,698 @@ reproducible gene expression signatures capable of accurately distinguishing
 tumor samples from healthy controls.")
     (license license:artistic2.0)))
 
+(define-public r-arrayexpress
+  (package
+    (name "r-arrayexpress")
+    (version "1.57.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "ArrayExpress" version))
+              (sha256
+               (base32
+                "1fzi951mjc4kbkkvlfvwlfrpfnjckkmw4xz4m5dapy1z2jkgp8w6"))))
+    (properties `((upstream-name . "ArrayExpress")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biobase
+           r-limma
+           r-oligo
+           r-xml))
+    (home-page "https://bioconductor.org/packages/ArrayExpress")
+    (synopsis "Building R objects from ArrayExpress datasets")
+    (description
+     "This package offers the possibility to access the ArrayExpress repository
+at @dfn{EBI} (European Bioinformatics Institute) and build Bioconductor data
+structures: @code{ExpressionSet}, @code{AffyBatch}, @code{NChannelSet}.")
+    (license license:artistic2.0)))
+
+(define-public r-asafe
+  (package
+    (name "r-asafe")
+    (version "1.24.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "ASAFE" version))
+              (sha256
+               (base32
+                "1q4i33rw1qb8bnvkl06izl4nyl9lzgwy8rwrmvbrz1c384pmy8yj"))))
+    (properties `((upstream-name . "ASAFE")))
+    (build-system r-build-system)
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/ASAFE")
+    (synopsis "Ancestry Specific Allele Frequency Estimation")
+    (description
+     "The @code{ASAFE} package contains a collection of functions that can be
+used to carry out an @dfn{EM} (Expectation–maximization) algorithm to estimate
+ancestry-specific allele frequencies for a bi-allelic genetic marker, e.g. an
+@dfn{SNP} (single nucleotide polymorphism) from genotypes and ancestry
+pairs.")
+    (license license:artistic2.0)))
+
+(define-public r-aseb
+  (package
+    (name "r-aseb")
+    (version "1.42.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "ASEB" version))
+              (sha256
+               (base32
+                "1kr6l2ma7wzy8i9dn86zx927yvx1l4bnkxhv97ra3sh5vr6m8ywa"))))
+    (properties `((upstream-name . "ASEB")))
+    (build-system r-build-system)
+    (home-page "https://bioconductor.org/packages/ASEB")
+    (synopsis "Predict acetylated lysine sites")
+    (description
+     "ASEB is an R package to predict lysine sites that can be acetylated by a
+specific @dfn{KAT} (K-acetyl-transferases) family.  Lysine acetylation is a
+well-studied posttranslational modification on kinds of proteins.  About four
+thousand lysine acetylation sites and over 20 lysine KATs have been
+identified.  However, which KAT is responsible for a given protein or lysine
+site acetylation is mostly unknown.  In this package, we use a
+@dfn{GSEA}-like (Gene Set Enrichment Analysis) method to make predictions.
+GSEA method was developed and successfully used to detect coordinated
+expression changes and find the putative functions of the long non-coding
+RNAs.")
+    (license license:gpl3+)))
+
+(define-public r-asgsca
+  (package
+    (name "r-asgsca")
+    (version "1.32.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "ASGSCA" version))
+              (sha256
+               (base32
+                "12wap8xbq6xl7p430yd9yy5kdhs15n7nmv2h3k9bsi0f4m6md02i"))))
+    (properties `((upstream-name . "ASGSCA")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-mass r-matrix))
+    (home-page "https://bioconductor.org/packages/ASGSCA")
+    (synopsis "Analysis of associations between multiple genotypes and traits")
+    (description
+     "The package @dfn{ASGSCA} (Association Study using Generalized Structured
+Component Analysis) provides tools to model and test the association between
+multiple genotypes and multiple traits, taking into account the prior
+biological knowledge.  Genes, and clinical pathways are incorporated in the
+model as latent variables.")
+    (license license:gpl3)))
+
+(define-public r-asics
+  (package
+    (name "r-asics")
+    (version "2.14.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "ASICS" version))
+              (sha256
+               (base32
+                "0c2b3gdza58vqhharhw8967p2w2knnrm5s2svvnnjbf67qbg45b7"))))
+    (properties `((upstream-name . "ASICS")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biocparallel
+           r-ggplot2
+           r-glmnet
+           r-gridextra
+           r-matrix
+           r-mvtnorm
+           r-pepsnmr
+           r-plyr
+           r-quadprog
+           r-ropls
+           r-summarizedexperiment
+           r-zoo))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/ASICS")
+    (synopsis "Automatic statistical identification in complex spectra")
+    (description
+     "ASICS quantifies concentration of metabolites in a complex spectrum.
+The identification of metabolites is performed by fitting a mixture model to
+the spectra of the library with a sparse penalty.")
+    (license license:gpl2+)))
+
+(define-public r-aspli
+  (package
+    (name "r-aspli")
+    (version "2.8.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "ASpli" version))
+              (sha256
+               (base32
+                "0gwp5ijpxjy6hd1090cmwbfrfac1qqrzxc06n1j89c0va7wm9l4k"))))
+    (properties `((upstream-name . "ASpli")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-annotationdbi
+           r-biocgenerics
+           r-biocstyle
+           r-data-table
+           r-dt
+           r-edger
+           r-genomicalignments
+           r-genomicfeatures
+           r-genomicranges
+           r-gviz
+           r-htmltools
+           r-igraph
+           r-iranges
+           r-limma
+           r-mass
+           r-pbmcapply
+           r-rsamtools
+           r-s4vectors
+           r-tidyr
+           r-upsetr))
+    (home-page "https://bioconductor.org/packages/ASpli")
+    (synopsis "Analysis of alternative splicing using RNA-Seq")
+    (description
+     "@dfn{AS} (alternative splicing) is a common mechanism of
+post-transcriptional gene regulation in eukaryotic organisms that expands the
+functional and regulatory diversity of a single gene by generating multiple
+mRNA isoforms that encode structurally and functionally distinct proteins.
+ASpli is an integrative pipeline and user-friendly R package that facilitates
+the analysis of changes in both annotated and novel AS events.  ASpli
+integrates several independent signals in order to deal with the complexity
+that might arise in splicing patterns.")
+    ;; The authors didn't specify any GPL version in description or in the
+    ;; sources.
+    (license (list license:gpl2+ license:gpl3+))))
+
+(define-public r-assessorf
+  (package
+    (name "r-assessorf")
+    (version "1.16.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "AssessORF" version))
+              (sha256
+               (base32
+                "125qkjsjyxp6zk3nzfamakyfgm7wd7w9vv1vn7xyyylpqpa8rpml"))))
+    (properties `((upstream-name . "AssessORF")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biostrings
+           r-decipher
+           r-genomicranges
+           r-iranges))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/AssessORF")
+    (synopsis "Assess gene predictions using proteomics and evolutionary conservation")
+    (description
+     "In order to assess the quality of a set of predicted genes for a genome,
+evidence must first be mapped to that genome.  Next, each gene must be
+categorized based on how strong the evidence is for or against that gene.  The
+AssessORF package provides the functions and class structures necessary for
+accomplishing those tasks, using proteomics hits and evolutionarily conserved
+start codons as the forms of evidence.")
+    (license license:gpl3)))
+
+(define-public r-asset
+  (package
+    (name "r-asset")
+    (version "2.16.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "ASSET" version))
+              (sha256
+               (base32
+                "13zwnjap4y0s3qqv10mv2i4mqan9nmkm2l29i448h1j3wwfq18j2"))))
+    (properties `((upstream-name . "ASSET")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-mass r-msm r-rmeta))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/ASSET")
+    (synopsis
+     "Subset-based association analysis of heterogeneous traits and subtypes")
+    (description
+     "This package is an R program for the subset-based analysis of
+heterogeneous traits and disease subtypes.  ASSET allows the user to search
+through all possible subsets of z-scores to identify the subset of traits
+giving the best meta-analyzed z-score.  Further, it returns a p-value
+adjusting for the multiple-testing involved in the search.  It also allows for
+searching for the best combination of disease subtypes associated with each
+variant.")
+    (license license:gpl2)))
+
+(define-public r-atena
+  (package
+    (name "r-atena")
+    (version "1.4.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "atena" version))
+              (sha256
+               (base32
+                "1a3qv66caz2pg67ff9c5424pygsgqnfx67ybzc3zkzaw4fj8cp54"))))
+    (properties `((upstream-name . "atena")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-annotationhub
+           r-biocgenerics
+           r-biocparallel
+           r-genomeinfodb
+           r-genomicalignments
+           r-genomicranges
+           r-iranges
+           r-matrix
+           r-rsamtools
+           r-s4vectors
+           r-scales
+           r-sparsematrixstats
+           r-squarem
+           r-summarizedexperiment))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/functionalgenomics/atena")
+    (synopsis "Analysis of transposable elements")
+    (description
+     "The atena package quantifies expression of @dfn{TEs} (transposable
+elements) from RNA-seq data through different methods, including ERVmap,
+TEtranscripts and Telescope.  A common interface is provided to use each of
+these methods, which consists of building a parameter object, calling the
+quantification function with this object and getting a
+@code{SummarizedExperiment} object as an output container of the quantified
+expression profiles.  The implementation allows quantifing TEs and gene
+transcripts in an integrated manner.")
+    (license license:artistic2.0)))
+
+(define-public r-atsnp
+  (package
+    (name "r-atsnp")
+    (version "1.14.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "atSNP" version))
+              (sha256
+               (base32
+                "12za1agpbjjg4i94mikbkdbwqnkzzwz07v0gwdc7lpa9899q2ycb"))))
+    (properties `((upstream-name . "atSNP")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biocfilecache
+           r-biocparallel
+           r-bsgenome
+           r-data-table
+           r-ggplot2
+           r-lifecycle
+           r-motifstack
+           r-rappdirs
+           r-rcpp
+           r-testthat))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/sunyoungshin/atSNP")
+    (synopsis
+     "Affinity test for identifying regulatory single nucleotide polymorphisms")
+    (description
+     "The atSNP package performs affinity tests of motif matches with the
+@dfn{SNP} (single nucleotide polymorphism) or the reference genomes and
+SNP-led changes in motif matches.")
+    (license license:gpl2)))
+
+(define-public r-attract
+  (package
+    (name "r-attract")
+    (version "1.50.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "attract" version))
+              (sha256
+               (base32
+                "0r5vykjqq33gchqv0wp2i6wpnk95cv26w5j4yqxcnw0bnqfhrgkm"))))
+    (properties `((upstream-name . "attract")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-annotationdbi
+           r-biobase
+           r-cluster
+           r-gostats
+           r-keggrest
+           r-limma
+           r-org-hs-eg-db
+           r-reactome-db))
+    (home-page "https://bioconductor.org/packages/attract")
+    (synopsis "Finding drivers of Kauffman's attractor landscape")
+    (description
+     "This package contains the functions to find the gene expression modules
+that represent the drivers of Kauffman's attractor landscape.  The modules are
+the core attractor pathways that discriminate between different cell types of
+groups of interest.  Each pathway has a set of synexpression groups, which show
+transcriptionally-coordinated changes in gene expression.")
+    (license license:lgpl2.0+)))
+
+(define-public r-awfisher
+  (package
+    (name "r-awfisher")
+    (version "1.12.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "AWFisher" version))
+              (sha256
+               (base32
+                "1psbxxrwb6mk2jwjw963vwdczb3i5590rcm7hk43kpiw45i1q1j9"))))
+    (properties `((upstream-name . "AWFisher")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-edger
+           r-limma))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/AWFisher")
+    (synopsis  "Fast computing for adaptively weighted fisher's method")
+    (description
+     "This package is an implementation of the Adaptively Weighted Fisher's
+method, including fast p-value computing, variability index, and
+meta-pattern.")
+    (license license:gpl3)))
+
+(define-public r-awst
+  (package
+    (name "r-awst")
+    (version "1.6.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "awst" version))
+              (sha256
+               (base32
+                "0dvzkqpjv7whns9q8zj6n2nyvnaw2ib7i53vf049n94x52vh9x15"))))
+    (properties `((upstream-name . "awst")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-summarizedexperiment))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/drisso/awst")
+    (synopsis "Asymmetric within-sample transformation")
+    (description
+     "This package @dfn{awst} (Asymmetric Within-Sample Transformation) that
+regularizes RNA-seq read counts and reduces the effect of noise on the
+classification of samples.  AWST comprises two main steps: standardization and
+smoothing.  These steps transform gene expression data to reduce the noise of
+the lowly expressed features, which suffer from background effects and low
+signal-to-noise ratio, and the influence of the highly expressed features,
+which may be the result of amplification bias and other experimental
+artifacts.")
+    (license license:expat)))
+
+(define-public r-baalchip
+  (package
+    (name "r-baalchip")
+    (version "1.24.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "BaalChIP" version))
+              (sha256
+               (base32
+                "16s67v6mkv14dkk1r7c50brm7198b84h87h1wrahmrrcnzq8pi0n"))))
+    (properties `((upstream-name . "BaalChIP")))
+    (build-system r-build-system)
+    (inputs (list perl)) ; extra/get.overlaps.v2_chrXY.perl
+    (propagated-inputs
+     (list r-coda
+           r-doby
+           r-doparallel
+           r-foreach
+           r-genomeinfodb
+           r-genomicalignments
+           r-genomicranges
+           r-ggplot2
+           r-iranges
+           r-reshape2
+           r-rsamtools
+           r-scales))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/BaalChIP")
+    (synopsis
+     "Analysis of allele-specific transcription factor binding in cancer genomes")
+    (description
+     "This package offers functions to process multiple @code{ChIP-seq BAM}
+files and detect allele-specific events.  It computes allele counts at
+individual variants (SNPs/SNVs), implements extensive @dfn{QC} (quality
+control) steps to remove problematic variants, and utilizes a Bayesian
+framework to identify statistically significant allele-specific events.
+BaalChIP is able to account for copy number differences between the two
+alleles, a known phenotypical feature of cancer samples.")
+    (license license:artistic2.0)))
+
+(define-public r-basespacer
+  (package
+    (name "r-basespacer")
+    (version "1.42.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "BaseSpaceR" version))
+              (sha256
+               (base32
+                "07pqs0jkwcbxavc65sanvhvzc9spkk46bqnwz162f3pvrz15b5h7"))))
+    (properties `((upstream-name . "BaseSpaceR")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-rcurl r-rjsonio))
+    (home-page "https://bioconductor.org/packages/BaseSpaceR")
+    (synopsis "R SDK for BaseSpace RESTful API")
+    (description
+     "This package provides an R interface to Illumina's BaseSpace cloud
+computing environment, enabling the fast development of data analysis and
+visualization tools.  Besides providing an easy to use set of tools for
+manipulating the data from BaseSpace, it also facilitates the access to R's
+rich environment of statistical and data analysis tools.")
+    (license license:asl2.0)))
+
+(define-public r-bac
+  (package
+    (name "r-bac")
+    (version "1.58.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "BAC" version))
+              (sha256
+               (base32
+                "00dkhns9n1x4wmlxjcw75h7iwwk37zlv1c2fi0g1mmsw1xvdjzp6"))))
+    (properties `((upstream-name . "BAC")))
+    (build-system r-build-system)
+    (home-page "https://bioconductor.org/packages/BAC")
+    (synopsis "Bayesian analysis of Chip-chip experiment")
+    (description
+     "This package uses a Bayesian hierarchical model to detect enriched
+regions from ChIP-chip experiments.  The common goal in analyzing this
+ChIP-chip data is to detect DNA-protein interactions from ChIP-chip
+experiments.  The BAC package has mainly been tested with Affymetrix tiling
+array data.  However, we expect it to work with other platforms (e.g. Agilent,
+Nimblegen, cDNA, etc.).  Note that BAC does not deal with normalization, so
+you will have to normalize your data beforehand.")
+    (license license:artistic2.0)))
+
+(define-public r-bader
+  (package
+    (name "r-bader")
+    (version "1.36.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "BADER" version))
+              (sha256
+               (base32
+                "1hkvmfik4m2yw5xg4k2g551l27i64blbsdvp1kmvvyix66p53hsr"))))
+    (properties `((upstream-name . "BADER")))
+    (build-system r-build-system)
+    (home-page "https://bioconductor.org/packages/BADER")
+    (synopsis
+     "Bayesian analysis of differential expression in RNA sequencing data")
+    (description
+     "The BADER package is intended for the analysis of RNA sequencing data.
+The algorithm fits a Bayesian hierarchical model for RNA sequencing count
+data.  BADER returns the posterior probability of differential expression for
+each gene between two groups A and B.  The joint posterior distribution of the
+variables in the model can be returned in the form of posterior samples, which
+can be used for further down-stream analyses such as gene set enrichment.")
+    (license license:gpl2)))
+
+(define-public r-badregionfinder
+  (package
+    (name "r-badregionfinder")
+    (version "1.26.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "BadRegionFinder" version))
+              (sha256
+               (base32
+                "0bsgdjchwsfc8aiwiacr454kw97dbymq6v450m1fx7hxmmpqz1sm"))))
+    (properties `((upstream-name . "BadRegionFinder")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biomart
+           r-genomicranges
+           r-rsamtools
+           r-s4vectors
+           r-variantannotation))
+    (home-page "https://bioconductor.org/packages/BadRegionFinder")
+    (synopsis "Identifying regions with bad coverage in sequence alignment data")
+    (description
+     "BadRegionFinder is a package for identifying regions with a bad,
+acceptable and good coverage in sequence alignment data available as bam
+files.  The whole genome may be considered as well as a set of target regions.
+Various visual and textual types of output are available.")
+    (license license:lgpl3)))
+
+(define-public r-bambu
+  (package
+    (name "r-bambu")
+    (version "3.0.5")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "bambu" version))
+              (sha256
+               (base32
+                "12rcbspy4ly714cyxbgd5v2m92vasksxm19m6hd4avasrhcr4d6l"))))
+    (properties `((upstream-name . "bambu")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biocgenerics
+           r-biocparallel
+           r-bsgenome
+           r-data-table
+           r-dplyr
+           r-genomeinfodb
+           r-genomicalignments
+           r-genomicfeatures
+           r-genomicranges
+           r-iranges
+           r-rcpp
+           r-rcpparmadillo
+           r-rsamtools
+           r-s4vectors
+           r-summarizedexperiment
+           r-tidyr
+           r-xgboost))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/GoekeLab/bambu")
+    (synopsis
+     "Isoform reconstruction and quantification for long read RNA-Seq data")
+    (description
+     "This R package is for multi-sample transcript discovery and
+quantification using long read RNA-Seq data.  You can use bambu after read
+alignment to obtain expression estimates for known and novel transcripts and
+genes.  The output from bambu can directly be used for visualisation and
+downstream analysis, such as differential gene expression or transcript
+usage.")
+    (license license:gpl3)))
+
+(define-public r-bandits
+  (package
+    (name "r-bandits")
+    (version "1.14.1")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "BANDITS" version))
+              (sha256
+               (base32
+                "0dbiz7zgdl3bqrwf4ffb73sc2dd8ygh76fakx5887a14azj8pk8x"))))
+    (properties `((upstream-name . "BANDITS")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biocparallel
+           r-data-table
+           r-doparallel
+           r-dorng
+           r-drimseq
+           r-foreach
+           r-ggplot2
+           r-mass
+           r-r-utils
+           r-rcpp
+           r-rcpparmadillo))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/SimoneTiberi/BANDITS")
+    (synopsis "Bayesian analysis of differential splicing")
+    (description
+     "BANDITS is a Bayesian hierarchical model for detecting differential
+splicing of genes and transcripts, via @dfn{DTU} (differential transcript
+usage), between two or more conditions.  The method uses a Bayesian
+hierarchical framework, which allows for sample specific proportions in a
+Dirichlet-Multinomial model, and samples the allocation of fragments to the
+transcripts.  Parameters are inferred via @dfn{MCMC} (Markov chain Monte
+Carlo) techniques and a DTU test is performed via a multivariate Wald test on
+the posterior densities for the average relative abundance of transcripts.")
+    (license license:gpl3+)))
+
+(define-public r-banocc
+  (package
+    (name "r-banocc")
+    (version "1.22.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "banocc" version))
+              (sha256
+               (base32
+                "0d7ss3df6zcfsh8kgy35ghxa6f27ynjhdbi6mdypgk9q24f64r78"))))
+    (properties `((upstream-name . "banocc")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-coda
+           r-mvtnorm
+           r-rstan
+           r-stringr))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/banocc")
+    (synopsis "Bayesian analysis of compositional covariance")
+    (description
+     "BAnOCC is a package designed for compositional data, where each sample
+sums to one.  It infers the approximate covariance of the unconstrained data
+using a Bayesian model coded with @code{rstan}.  It provides as output the
+@code{stanfit} object as well as posterior median and credible interval
+estimates for each correlation element.")
+    (license license:expat)))
+
+(define-public r-barcodetrackr
+  (package
+    (name "r-barcodetrackr")
+    (version "1.6.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "barcodetrackR" version))
+              (sha256
+               (base32
+                "1b3z83nkl8csxs88rcbmkkfjps71mwnylvpy3kjzyi02xw0kh0c1"))))
+    (properties `((upstream-name . "barcodetrackR")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-circlize
+           r-cowplot
+           r-dplyr
+           r-ggdendro
+           r-ggplot2
+           r-ggridges
+           r-magrittr
+           r-plyr
+           r-proxy
+           r-rcolorbrewer
+           r-rlang
+           r-s4vectors
+           r-scales
+           r-shiny
+           r-summarizedexperiment
+           r-tibble
+           r-tidyr
+           r-vegan
+           r-viridis))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/dunbarlabNIH/barcodetrackR")
+    (synopsis "Functions for analyzing cellular barcoding data")
+    (description
+     "This package is developed for the analysis and visualization of clonal
+tracking data.  The required data is formed by samples and tag abundances in
+matrix form, usually from cellular barcoding experiments, integration site
+retrieval analyses, or similar technologies.")
+    (license license:cc0)))
+
 (define-public r-biocversion
   (package
     (name "r-biocversion")
-    (version "3.15.2")
+    (version "3.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocVersion" version))
        (sha256
         (base32
-         "0rs4nyza4hqqk204d037gi013135wgfhx5asq2dsdjc9vk5nwzfn"))))
+         "1djp23y131dyx4g22f9r7an177bq0mky94bvpqvc8b14166g0ynw"))))
     (properties `((upstream-name . "BiocVersion")))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/BiocVersion/")
@@ -2293,13 +3578,13 @@ of Bioconductor.")
 (define-public r-biocgenerics
   (package
     (name "r-biocgenerics")
-    (version "0.42.0")
+    (version "0.44.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocGenerics" version))
               (sha256
                (base32
-                "0iv9bnpw2hycndwbmjsszqfwrksz6dfr6qcz78jkssc9ldsgmdhc"))))
+                "17dhr7vaph8dnvyklszyas7y8i64mxqxhnfhb6q3l47gq5if8645"))))
     (properties
      `((upstream-name . "BiocGenerics")))
     (build-system r-build-system)
@@ -2310,16 +3595,88 @@ of Bioconductor.")
 packages.")
     (license license:artistic2.0)))
 
+(define-public r-breakpointr
+  (package
+    (name "r-breakpointr")
+    (version "1.16.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "breakpointR" version))
+              (sha256
+               (base32
+                "0j1f43lhgkapjyxlil9fflqh9nf3andhmvirdcv45y60wvljn4gx"))))
+    (properties `((upstream-name . "breakpointR")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biocgenerics
+           r-breakpointrdata
+           r-cowplot
+           r-doparallel
+           r-foreach
+           r-genomeinfodb
+           r-genomicalignments
+           r-genomicranges
+           r-ggplot2
+           r-gtools
+           r-iranges
+           r-rsamtools
+           r-s4vectors))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/daewoooo/BreakPointR")
+    (synopsis "Find breakpoints in Strand-seq data")
+    (description
+     "This package implements functions for finding breakpoints, plotting and
+export of Strand-seq data.")
+    (license license:expat)))
+
+(define-public r-cardelino
+  (package
+    (name "r-cardelino")
+    (version "1.0.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "cardelino" version))
+              (sha256
+               (base32
+                "1ma4clkrkrjvy12ln2d2smyzzsz9y9554f5wgwmh9kv6s4xc66qs"))))
+    (properties `((upstream-name . "cardelino")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-combinat
+                             r-genomeinfodb
+                             r-genomicranges
+                             r-ggplot2
+                             r-ggtree
+                             r-matrix
+                             r-matrixstats
+                             r-pheatmap
+                             r-s4vectors
+                             r-snpstats
+                             r-variantannotation
+                             r-vcfr))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/single-cell-genetics/cardelino")
+    (synopsis "Clone identification from single cell data")
+    (description
+     "This package provides methods to infer clonal tree configuration for a
+population of cells using single-cell RNA-seq data (scRNA-seq), and possibly
+other data modalities.  Methods are also provided to assign cells to inferred
+clones and explore differences in gene expression between clones.  These
+methods can flexibly integrate information from imperfect clonal trees
+inferred based on bulk exome-seq data, and sparse variant alleles expressed in
+scRNA-seq data.  A flexible beta-binomial error model that accounts for
+stochastic dropout events as well as systematic allelic imbalance is used.")
+    (license license:gpl3)))
+
 (define-public r-coverageview
   (package
     (name "r-coverageview")
-    (version "1.34.0")
+    (version "1.36.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "CoverageView" version))
               (sha256
                (base32
-                "0mh66l4yh6rpd1r7qbqwh5jkklqyvpfiap0zcqhz9kimssm2pbbp"))))
+                "0cqvwp0ybxgnk9kif3ly780v23pwv4cyh46kk47gxcxqqkjv36ld"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-s4vectors
@@ -2340,13 +3697,13 @@ how the coverage distributed across the genome.")
 (define-public r-cummerbund
   (package
    (name "r-cummerbund")
-   (version "2.38.0")
+   (version "2.40.0")
    (source (origin
              (method url-fetch)
              (uri (bioconductor-uri "cummeRbund" version))
              (sha256
               (base32
-               "1p4anmi436zykp0ir307g75g23kj8b7shxg4r65qq6zdwflphm0q"))))
+               "1fzkhnlgv4zd0slr12d5aichyxsca86p82fyjymiz7f5fqdvqmd9"))))
    (build-system r-build-system)
    (propagated-inputs
     (list r-biobase
@@ -2367,17 +3724,80 @@ data.  In addition, provides numerous plotting functions for commonly
 used visualizations.")
    (license license:artistic2.0)))
 
+(define-public r-dama
+  (package
+    (name "r-dama")
+    (version "1.70.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "daMA" version))
+              (sha256
+               (base32
+                "062nxfry9w674ja3q9zs4df2hvf4wws9jdqpy84g6nb0309vbhqf"))))
+    (properties `((upstream-name . "daMA")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-mass))
+    (home-page "https://bioconductor.org/packages/release/bioc/html/daMA.html")
+    (synopsis
+     "Efficient design and analysis of factorial two-colour microarray data")
+    (description
+     "This package contains functions for the efficient design of factorial
+two-colour microarray experiments and for the statistical analysis of
+factorial microarray data.")
+    (license license:gpl2+)))
+
+(define-public r-damefinder
+  (package
+    (name "r-damefinder")
+    (version "1.10.1")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "DAMEfinder" version))
+              (sha256
+               (base32
+                "1cgykb70mxnhilwwp1jr4dr523zvjxpix173s4ldfh49064gzwc1"))))
+    (properties `((upstream-name . "DAMEfinder")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biocgenerics
+           r-biostrings
+           r-bumphunter
+           r-cowplot
+           r-genomeinfodb
+           r-genomicalignments
+           r-genomicranges
+           r-ggplot2
+           r-iranges
+           r-limma
+           r-plyr
+           r-readr
+           r-reshape2
+           r-rsamtools
+           r-s4vectors
+           r-stringr
+           r-summarizedexperiment
+           r-variantannotation))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/DAMEfinder")
+    (synopsis "Differential allelicly methylated regions")
+    (description
+     "This package offers functionality for taking methtuple or Bismark
+outputs to calculate @acronym{ASM, Allele-Specific Methylation} scores and
+compute @acronym{DAMEs, Differential Allelicly MEthylated} regions.  It also
+offers nice visualization of methyl-circle plots.")
+    (license license:expat)))
+
 (define-public r-dearseq
   (package
     (name "r-dearseq")
-    (version "1.8.1")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "dearseq" version))
        (sha256
         (base32
-         "1f144k5gsclcmsnlsbisr2mivk91dbkci83wx1kznw6i15p4cpj1"))))
+         "1f9hz4jp862jm1grf4qzdvnzp17ri0n1rhfafgkc1j73z6whw1b0"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-compquadform
@@ -2390,6 +3810,7 @@ used visualizations.")
            r-pbapply
            r-reshape2
            r-rlang
+           r-scattermore
            r-statmod
            r-survey
            r-tibble
@@ -2405,16 +3826,55 @@ heteroscedasticity through precision weights.  Perform both gene-wise and gene
 set analyses, and can deal with repeated or longitudinal data.")
     (license license:gpl2)))
 
+(define-public r-debcam
+  (package
+    (name "r-debcam")
+    (version "1.16.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "debCAM" version))
+              (sha256
+               (base32
+                "09dm861adbxdy3ncfdxq46wjr4hpn56c66n64xm9gwzkzsrxyc2a"))))
+    (properties `((upstream-name . "debCAM")))
+    (build-system r-build-system)
+    (inputs (list openjdk))
+    (propagated-inputs
+     (list r-apcluster
+           r-biobase
+           r-biocparallel
+           r-corpcor
+           r-dmwr2
+           r-geometry
+           r-nmf
+           r-nnls
+           r-pcapp
+           r-rjava
+           r-summarizedexperiment))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/debCAM")
+    (synopsis "Deconvolution by convex analysis of mixtures")
+    (description
+     "This package is an R implementation for fully unsupervised deconvolution
+of complex tissues.  DebCAM provides basic functions to perform unsupervised
+deconvolution on mixture expression profiles by @acronym{CAM, Convex Analysis
+of Mixtures} and some auxiliary functions to help understand the
+subpopulation- specific results.  It also implements functions to perform
+supervised deconvolution based on prior knowledge of molecular markers, S
+matrix or A matrix.  Combining molecular markers from CAM and from prior
+knowledge can achieve semi-supervised deconvolution of mixtures.")
+    (license license:gpl2)))
+
 (define-public r-decipher
   (package
     (name "r-decipher")
-    (version "2.24.0")
+    (version "2.26.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "DECIPHER" version))
               (sha256
                (base32
-                "045q2bfzgq1yzhyrzvrhrnmlpka4gikrajxxwv05szksy5nvp7q5"))))
+                "01hzxd5f5v2kspx5jd7l21bn87cfgm9aah3zd4d6kyxv98h5a3n1"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biostrings
@@ -2429,16 +3889,187 @@ set analyses, and can deal with repeated or longitudinal data.")
 biological sequences.")
     (license license:gpl3)))
 
+(define-public r-deco
+  (package
+    (name "r-deco")
+    (version "1.13.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "deco" version))
+              (sha256
+               (base32
+                "0d4abif3v62cbas6hl7pfw8q8jihh7nsra76k9cm6kz54qw4fbnw"))))
+    (properties `((upstream-name . "deco")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-ade4
+           r-annotationdbi
+           r-biobase
+           r-biocparallel
+           r-biocstyle
+           r-cluster
+           r-foreign
+           r-gdata
+           r-ggplot2
+           r-gplots
+           r-gridextra
+           r-limma
+           r-locfit
+           r-made4
+           r-rcolorbrewer
+           r-reshape2
+           r-scatterplot3d
+           r-sfsmisc
+           r-summarizedexperiment))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/fjcamlab/deco")
+    (synopsis "Decomposing heterogeneous cohorts using omic data profiling")
+    (description
+     "This package discovers differential features in hetero- and homogeneous
+omic data by a two-step method including subsampling LIMMA and NSCA.  DECO
+reveals feature associations to hidden subclasses not exclusively related to
+higher deregulation levels.")
+    (license license:gpl3+)))
+
+(define-public r-decomplexdisease
+  (package
+    (name "r-decomplexdisease")
+    (version "1.18.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "DEComplexDisease" version))
+              (sha256
+               (base32
+                "12gw9b0gdwyih51j2gzay6vxhycgc52n8svd0slv6wsbw5rc19lh"))))
+    (properties `((upstream-name . "DEComplexDisease")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biocparallel
+           r-complexheatmap
+           r-deseq2
+           r-edger
+           r-rcpp
+           r-summarizedexperiment))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/DEComplexDisease")
+    (synopsis "Investigations of complex diseases by bi-clustering analysis")
+    (description
+     "DEComplexDisease is designed to find the @acronym{DEGs, Differential
+Expressed Genes} for complex disease, which is characterized by the
+heterogeneous genomic expression profiles.  Different from the established DEG
+analysis tools, it does not assume the patients of complex diseases to share
+the common DEGs.  By applying a bi-clustering algorithm, DEComplexDisease
+finds the DEGs shared by as many patients.  Applying the DEComplexDisease
+analysis results, users are possible to find the patients affected by the same
+mechanism based on the shared signatures.")
+    (license license:gpl3)))
+
+(define-public r-decomptumor2sig
+  (package
+    (name "r-decomptumor2sig")
+    (version "2.14.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "decompTumor2Sig" version))
+              (sha256
+               (base32
+                "0agvmgwyk458lhhhspd8243n4897f0q7jf9yqhwsl5wi8011vmqd"))))
+    (properties `((upstream-name . "decompTumor2Sig")))
+    (build-system r-build-system)
+    (inputs (list perl))                ;script/extractSpecColumns.pl
+    (propagated-inputs
+     (list r-biocgenerics
+           r-biostrings
+           r-bsgenome-hsapiens-ucsc-hg19
+           r-data-table
+           r-genomeinfodb
+           r-genomicfeatures
+           r-genomicranges
+           r-ggplot2
+           r-ggseqlogo
+           r-gridextra
+           r-matrix
+           r-plyr
+           r-quadprog
+           r-readxl
+           r-s4vectors
+           r-summarizedexperiment
+           r-txdb-hsapiens-ucsc-hg19-knowngene
+           r-variantannotation))
+    (native-inputs (list r-knitr))
+    (home-page "https://rmpiro.net/decompTumor2Sig/")
+    (synopsis "Decomposition of individual tumors into mutational signatures")
+    (description
+     "The package uses quadratic programming for signature refitting, i.e., to
+decompose the mutation catalog from an individual tumor sample into a set of
+given mutational signatures (either Alexandrov-model signatures or
+Shiraishi-model signatures), computing weights that reflect the contributions
+of the signatures to the mutation load of the tumor.")
+    (license license:gpl2)))
+
+(define-public r-deconrnaseq
+  (package
+    (name "r-deconrnaseq")
+    (version "1.40.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "DeconRNASeq" version))
+              (sha256
+               (base32
+                "05rwqchfspy8i9fcj9526rl5vvk0rrgr95nvxzdj0sa2136my8y4"))))
+    (properties `((upstream-name . "DeconRNASeq")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-ggplot2
+           r-limsolve
+           r-pcamethods))
+    (home-page "https://bioconductor.org/packages/DeconRNASeq")
+    (synopsis
+     "Deconvolution of heterogeneous tissue samples for mRNA-Seq data")
+    (description
+     "DeconSeq is an R package for deconvolution of heterogeneous tissues
+based on mRNA-Seq data.  It models the expression levels from heterogeneous
+cell populations in mRNA-Seq as the weighted average of expression from
+different constituting cell types and predicted cell type proportions of
+single expression profiles.")
+    (license license:gpl2)))
+
+(define-public r-decontam
+  (package
+    (name "r-decontam")
+    (version "1.18.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "decontam" version))
+              (sha256
+               (base32
+                "0bk7ia2flnxwa99b8mf3xdvap3xqa4pvpsrgbnyapxbaqxr5zf82"))))
+    (properties `((upstream-name . "decontam")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-ggplot2 r-reshape2))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/benjjneb/decontam")
+    (synopsis
+     "Identification of contaminants in marker-gene and metagenomics data")
+    (description
+     "This package offers simple statistical identification of contaminating
+sequence features in marker-gene or metagenomics data.  It works on any kind
+of feature derived from environmental sequencing data (e.g. ASVs, OTUs,
+taxonomic groups, MAGs, etc).  Requires DNA quantitation data or sequenced
+negative control samples.")
+    (license license:artistic2.0)))
+
 (define-public r-deconvr
   (package
     (name "r-deconvr")
-    (version "1.2.0")
+    (version "1.4.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "deconvR" version))
               (sha256
                (base32
-                "091z3lncamscsvzj63zzbw7dr7vnkn0jwfkm5ljq4112w4rxgrm3"))))
+                "1jz7q4rv3m85bcvarjhqsyc2330fynb0wr5ajd2qffznczk846xb"))))
     (properties `((upstream-name . "deconvR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2454,6 +4085,7 @@ biological sequences.")
            r-mass
            r-matrixstats
            r-methylkit
+           r-minfi
            r-nnls
            r-quadprog
            r-rsq
@@ -2476,13 +4108,13 @@ make mapping WGBS data to their probe IDs easier.")
 (define-public r-decoupler
   (package
     (name "r-decoupler")
-    (version "2.2.2")
+    (version "2.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "decoupleR" version))
        (sha256
-        (base32 "0q1w8yw3bwx8ai5z8rw8lz97w4cplxijq93634hza2vgkig1ck9m"))))
+        (base32 "1872pi2v9gymdpqdhab10ash4b2w8sbk1p635lf0p6s4679syhdi"))))
     (properties `((upstream-name . "decoupleR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2517,13 +4149,13 @@ targeted by a kinase.")
 (define-public r-deepsnv
   (package
     (name "r-deepsnv")
-    (version "1.42.1")
+    (version "1.44.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "deepSNV" version))
               (sha256
                (base32
-                "0bgj1grv3a5bqhcdsw445x49kl3pz367svy6fnrzfsk9bmj46kgn"))))
+                "051xcg9lx8plbfhiacrv1wsxfac0qqspysq960ppibkf4m8crk81"))))
     (properties `((upstream-name . "deepSNV")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2553,13 +4185,13 @@ bases such as COSMIC.")
 (define-public r-delayedarray
   (package
     (name "r-delayedarray")
-    (version "0.22.0")
+    (version "0.24.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "DelayedArray" version))
               (sha256
                (base32
-                "11id63qza9dxl1364gllqafxmx25a0q22jv5q8h709bgc3f0grqy"))))
+                "0nl1v0mxb759wiia2rsxay0cv0q631gqyzgaa10s175lhzsb8r6p"))))
     (properties
      `((upstream-name . "DelayedArray")))
     (build-system r-build-system)
@@ -2583,13 +4215,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns),
 (define-public r-derfinderhelper
   (package
     (name "r-derfinderhelper")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "derfinderHelper" version))
        (sha256
-        (base32 "0r7zbx5bfmh5cjs12y8d9qwz53nz340gdy3sx7zcn4rzn7rpslp5"))))
+        (base32 "118rjmqy53viczdwj70kaszkpg2r2zbq60k49jg7fqb81prdwy04"))))
     (properties `((upstream-name . "derfinderHelper")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2608,13 +4240,13 @@ calculation in parallel.")
 (define-public r-drimseq
   (package
     (name "r-drimseq")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DRIMSeq" version))
        (sha256
-        (base32 "1dph483ij43ayw0z5dbnp6gwp53ka7k5si1hp3miac7z8dqzv94l"))))
+        (base32 "0cj3fyb99fh30f35ra1gpvzwplszbwvwk33ppgyh1zx2axsx164w"))))
     (properties `((upstream-name . "DRIMSeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2643,13 +4275,13 @@ results.")
 (define-public r-bluster
   (package
    (name "r-bluster")
-   (version "1.6.0")
+   (version "1.8.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "bluster" version))
             (sha256
              (base32
-              "1g496yc7mdhshf6r0n8xhj7ax936ia5z2cx72lqyk2vzzzl5c4v8"))))
+              "1xi9vl09nm95l35kb9n3pn3j9qxw8976lss3cx0ppwnxd2mjr6vy"))))
    (properties `((upstream-name . "bluster")))
    (build-system r-build-system)
    (propagated-inputs
@@ -2673,13 +4305,13 @@ and evaluate clustering results.")
 (define-public r-ideoviz
   (package
     (name "r-ideoviz")
-    (version "1.32.0")
+    (version "1.34.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "IdeoViz" version))
               (sha256
                (base32
-                "1wwh3ifdijhpm58lw7cmnx084xwfxnc7i0206w8rhrjnvnq6ljh3"))))
+                "0jpj8bkfm3jcb5fj0xhh13vqh2dcgdgi4i1qk3wx1301irkk7fgf"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase
@@ -2697,14 +4329,14 @@ arbitrary genomic intervals along chromosomal ideogram.")
 (define-public r-infercnv
   (package
     (name "r-infercnv")
-    (version "1.12.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "infercnv" version))
        (sha256
         (base32
-         "01f021fdxm058733rky46dlvqg7dmf5mn5x9lnq0fspp5665w3bl"))))
+         "11hgw6c67gd3ih5q14a520sjmnlv56qw19z0i6s5pz2slmgflpry"))))
     (properties `((upstream-name . "infercnv")))
     (build-system r-build-system)
     (inputs (list python))
@@ -2728,15 +4360,16 @@ arbitrary genomic intervals along chromosomal ideogram.")
            r-gplots
            r-gridextra
            r-hiddenmarkov
-           r-leiden
+           r-igraph
            r-matrix
            r-paralleldist
            r-phyclust
            r-rann
            r-rcolorbrewer
-           r-reshape
+           r-reshape2
            r-rjags
            r-singlecellexperiment
+           r-seurat
            r-summarizedexperiment
            r-tidyr))
     (native-inputs (list r-knitr))
@@ -2756,13 +4389,13 @@ over-abundant or less-abundant as compared to that of normal cells.")
 (define-public r-iranges
   (package
     (name "r-iranges")
-    (version "2.30.1")
+    (version "2.32.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "IRanges" version))
               (sha256
                (base32
-                "1r01c9lczkchgd9hbxxd6wrd5avhy52mfqjck7l9avjq1jimvzv3"))))
+                "0jvavhl6p2di0n5176gg7shfmpg79rngl2gaw423icswdf8kay89"))))
     (properties
      `((upstream-name . "IRanges")))
     (build-system r-build-system)
@@ -2784,13 +4417,13 @@ possible.")
 (define-public r-isoformswitchanalyzer
   (package
     (name "r-isoformswitchanalyzer")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "IsoformSwitchAnalyzeR" version))
        (sha256
-        (base32 "0n1gb9azxa1mxpsqvw3i3kf72f45nyjj1kgwwrzhd88n3g63lvkd"))))
+        (base32 "06kcx0a7xxzqhf4y8l69my5chh06sfahsaz6anhana7shym3yif5"))))
     (properties `((upstream-name . "IsoformSwitchAnalyzeR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2942,18 +4575,19 @@ mapping.")
 (define-public r-nmf
   (package
     (name "r-nmf")
-    (version "0.24.0")
+    (version "0.25")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "NMF" version))
        (sha256
         (base32
-         "14yxra6in5c1md5nr75y8cdmh9pg0lxqabqflvlhgg1vbg9i2628"))))
+         "0kdl7yz4v7pms6y2lff4x5w7pwkx54488qx0v539qmvcbxv1if98"))))
     (properties `((upstream-name . "NMF")))
     (build-system r-build-system)
     (propagated-inputs
      (list r-cluster
+           r-codetools
            r-biobase
            r-biocmanager
            r-bigmemory ; suggested
@@ -2964,7 +4598,6 @@ mapping.")
            r-foreach
            r-ggplot2
            r-gridbase
-           r-pkgmaker
            r-rcolorbrewer
            r-registry
            r-reshape2
@@ -2986,14 +4619,14 @@ performing parallel computations on multicore machines.")
 (define-public r-affy
   (package
     (name "r-affy")
-    (version "1.74.0")
+    (version "1.76.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affy" version))
        (sha256
         (base32
-         "02l77y4d4m4jwgkb3jdaskv6shmba5292whp0i29mg9asxv4rdc7"))))
+         "1iix9mq4aph6avs2qr64a7hip461cif56k6npvs5g69nj3rn50gj"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-affyio
@@ -3014,14 +4647,14 @@ analysis.")
 (define-public r-affycomp
   (package
     (name "r-affycomp")
-    (version "1.72.0")
+    (version "1.74.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affycomp" version))
        (sha256
         (base32
-         "0aq5p56sqpvba0yhgd75302s9bazchh1izgymng6cpb78y5wfpj0"))))
+         "18bxnjcl7cbgwm3yf58608ghwnpci94xgil11zmbpgzgrpv9pkrs"))))
     (properties `((upstream-name . "affycomp")))
     (build-system r-build-system)
     (propagated-inputs (list r-biobase))
@@ -3035,14 +4668,14 @@ measures for Affymetrix Oligonucleotide Arrays.")
 (define-public r-affycompatible
   (package
     (name "r-affycompatible")
-    (version "1.56.0")
+    (version "1.58.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AffyCompatible" version))
        (sha256
         (base32
-         "0x3lj1jgqq67389rzfklah5p878ns9b4fpdpz455m2gq9sk7qsda"))))
+         "1bg7iqasvfsgd9x3ykgpblqnz1q06g3ifmzj4jf2kn8kxj63wfbl"))))
     (properties
      `((upstream-name . "AffyCompatible")))
     (build-system r-build-system)
@@ -3080,14 +4713,14 @@ Command Console} (AGCC)-compatible sample annotation files.")
 (define-public r-affycontam
   (package
     (name "r-affycontam")
-    (version "1.54.0")
+    (version "1.56.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affyContam" version))
        (sha256
         (base32
-         "1pyd4rj6pp139kvhh97whi4afvx029w5lglr4mnscw7m3f618v0p"))))
+         "0phf9rvxr45zq9m5rcjsiixmj9ilz518l628l8cd1hzfdk240ffy"))))
     (properties `((upstream-name . "affyContam")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3103,14 +4736,14 @@ problems in CEL-level data to help evaluate performance of quality metrics.")
 (define-public r-affycoretools
   (package
     (name "r-affycoretools")
-    (version "1.68.1")
+    (version "1.70.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affycoretools" version))
        (sha256
         (base32
-         "05x64hy5jpmg973biwq4q9gzy1n0iqc0pxrix1f6bri1w6vil3ww"))))
+         "17slls8dihjnpm6bynic8cm2fbnfl5iqwimz0wz7c9x44d1bxi4l"))))
     (properties `((upstream-name . "affycoretools")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3145,14 +4778,14 @@ to streamline the more common analyses that a Biostatistician might see.")
 (define-public r-affyio
   (package
     (name "r-affyio")
-    (version "1.66.0")
+    (version "1.68.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affyio" version))
        (sha256
         (base32
-         "19cw82qvzkz6vh2gm302y7digsf6xif7c9l2q9s6lkx2yflqpgfp"))))
+         "1bdcz9sz4khs7p4ddryc4ir0fwcjrkwqka8y0c9n36ykiv4myfib"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-zlibbioc))
@@ -3169,14 +4802,14 @@ CDF file formats.")
 (define-public r-affxparser
   (package
     (name "r-affxparser")
-    (version "1.68.1")
+    (version "1.70.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affxparser" version))
        (sha256
         (base32
-         "16x92gwsy7zdyz4md4cw847xn2ymqd6gqsn0rlr2nnf3qmnjnils"))))
+         "0p42rpyh96aph9jr8kiyjvv860jn7m7ji2nrib2vr2nl0jyaxqjs"))))
     (properties `((upstream-name . "affxparser")))
     (build-system r-build-system)
     (home-page "https://github.com/HenrikBengtsson/affxparser")
@@ -3197,14 +4830,14 @@ structure.")
 (define-public r-annotate
   (package
     (name "r-annotate")
-    (version "1.74.0")
+    (version "1.76.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "annotate" version))
        (sha256
         (base32
-         "0x6vddpiw2g713vicf70198x8dlrwf36p8jjygdsfnl56ls5bh2g"))))
+         "06jmnv36y3n6pl1vs6mp14sgyzl4l37g13diaa49k7qwp1kdpl3a"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotationdbi
@@ -3224,13 +4857,13 @@ microarrays.")
 (define-public r-annotationdbi
   (package
     (name "r-annotationdbi")
-    (version "1.58.0")
+    (version "1.60.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AnnotationDbi" version))
               (sha256
                (base32
-                "15cwy7lic89jwl3dr7j4pb5bx457jdpvzvylr71624s0p0j9rgwn"))))
+                "1srv0jizmwgmsmgb9cfgy5nbgd3jsgxgzzax6wfsahckb5zihrqp"))))
     (properties
      `((upstream-name . "AnnotationDbi")))
     (build-system r-build-system)
@@ -3254,13 +4887,13 @@ annotation data packages using SQLite data storage.")
 (define-public r-annotationfilter
   (package
     (name "r-annotationfilter")
-    (version "1.20.0")
+    (version "1.22.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AnnotationFilter" version))
               (sha256
                (base32
-                "082lpcd6yr2nkxndlck2wqqd3nfdx7lnpw8barxgv41q4l7v4ald"))))
+                "0m16kfssxbblf03ykawkmqa038cl90prhb23k6y88g2hwm00wynk"))))
     (properties
      `((upstream-name . "AnnotationFilter")))
     (build-system r-build-system)
@@ -3279,14 +4912,14 @@ used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.")
 (define-public r-annotationforge
   (package
     (name "r-annotationforge")
-    (version "1.38.0")
+    (version "1.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AnnotationForge" version))
        (sha256
         (base32
-         "18rcfadxdaggyjj3rj17nbvgddlqs6zlr5jmq9a02kin59czvzz8"))))
+         "15shh8rmcx69g3zd256720vh0c3qbly5zrvwm463dws41cjla48x"))))
     (properties
      `((upstream-name . "AnnotationForge")))
     (build-system r-build-system)
@@ -3311,14 +4944,14 @@ databases.  Packages produced are intended to be used with AnnotationDbi.")
 (define-public r-annotationhub
   (package
     (name "r-annotationhub")
-    (version "3.4.0")
+    (version "3.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AnnotationHub" version))
        (sha256
         (base32
-         "03dmbx43rsv9xv94lk12gpraq47ryc13jijwma3q05hl9wn8xjxs"))))
+         "1hk02q6mwx49khbhydndfa1qry8ylhmwz2dff8845a510hm0di7n"))))
     (properties `((upstream-name . "AnnotationHub")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3352,14 +4985,14 @@ by the user, helping with quick and reproducible access.")
 (define-public r-aroma-light
   (package
     (name "r-aroma-light")
-    (version "3.26.0")
+    (version "3.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "aroma.light" version))
        (sha256
         (base32
-         "1240v9wvsf205g998ms19hncki8g6shidg09dy5np9pqpiix4vys"))))
+         "01g9vfkmpfkn9nv71jyybq93lid6x93jbadjahngy98w67n3sin4"))))
     (properties `((upstream-name . "aroma.light")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3376,14 +5009,14 @@ classes.")
 (define-public r-bamsignals
   (package
     (name "r-bamsignals")
-    (version "1.28.0")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bamsignals" version))
        (sha256
         (base32
-         "0ywbxq829hclhr5bb6p77rspxvfs580zlwd2f5kr3an6rdgyx9ky"))))
+         "059pkm5pg9ssd0l8xrm13d0hscqnmlqcb4qb5p4fbzgx6088zg05"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biocgenerics
@@ -3406,13 +5039,13 @@ paired-end data.")
 (define-public r-biobase
   (package
     (name "r-biobase")
-    (version "2.56.0")
+    (version "2.58.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Biobase" version))
               (sha256
                (base32
-                "1mnxky78an079p60427cjvk4fzilp0xzy6b85fq274qvdcrz8jbv"))))
+                "0rp541nphbcya6kbk1nzrrb05g5m6pxb3yqz5cj873di9vsqlyfv"))))
     (properties
      `((upstream-name . "Biobase")))
     (build-system r-build-system)
@@ -3428,13 +5061,13 @@ on Bioconductor or which replace R functions.")
 (define-public r-biomart
   (package
     (name "r-biomart")
-    (version "2.52.0")
+    (version "2.54.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "biomaRt" version))
               (sha256
                (base32
-                "0yn3kanyrplc89a900xiz33nw1v23mkljvd5isizgs8gzvwzf8xg"))))
+                "0c6agi652kbffqwd1r3c22ncisqaiy3gqbc9fz13767rr71im6lq"))))
     (properties
      `((upstream-name . "biomaRt")))
     (build-system r-build-system)
@@ -3513,13 +5146,13 @@ only one command.")
 (define-public r-biocparallel
   (package
     (name "r-biocparallel")
-    (version "1.30.3")
+    (version "1.32.5")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocParallel" version))
               (sha256
                (base32
-                "1rs3wmasl9mx7f399iclvm0bnvggvjj2a88zbi294r5m8wxqlc92"))))
+                "1yd6ln9cl3dcvfziar52fkvqi2lzm31l7j21r1rwl1mpkz0xapir"))))
     (properties
      `((upstream-name . "BiocParallel")))
     (build-system r-build-system)
@@ -3531,18 +5164,16 @@ only one command.")
              ;; Remove generated documentation.
              (for-each delete-file
                        '("inst/doc/BiocParallel_BatchtoolsParam.pdf"
-                         "inst/doc/Introduction_To_BiocParallel.pdf"
                          "inst/doc/Errors_Logs_And_Debugging.pdf"
                          "inst/doc/BiocParallel_BatchtoolsParam.R"
                          "inst/doc/Introduction_To_BiocParallel.R"
-                         "inst/doc/Errors_Logs_And_Debugging.R"))
+                         "inst/doc/Errors_Logs_And_Debugging.R"
+                         "inst/doc/Random_Numbers.R"))
 
              ;; Remove time-dependent macro
              (substitute* '("inst/doc/BiocParallel_BatchtoolsParam.Rnw"
-                            "inst/doc/Introduction_To_BiocParallel.Rnw"
                             "inst/doc/Errors_Logs_And_Debugging.Rnw"
                             "vignettes/BiocParallel_BatchtoolsParam.Rnw"
-                            "vignettes/Introduction_To_BiocParallel.Rnw"
                             "vignettes/Errors_Logs_And_Debugging.Rnw")
                (("\\today") "later"))
 
@@ -3552,7 +5183,7 @@ only one command.")
                 (string-append
                  m "; if (!is.na(Sys.getenv(\"SOURCE_DATE_EPOCH\"))) {set.seed(100)}\n"))))))))
     (propagated-inputs
-     (list r-bh r-codetools r-futile-logger r-snow))
+     (list r-bh r-cpp11 r-codetools r-futile-logger r-snow))
     (native-inputs
      (list r-knitr))
     (home-page "https://bioconductor.org/packages/BiocParallel")
@@ -3566,13 +5197,13 @@ objects.")
 (define-public r-biostrings
   (package
     (name "r-biostrings")
-    (version "2.64.0")
+    (version "2.66.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Biostrings" version))
               (sha256
                (base32
-                "1sz52hz89l9w2y2bvyis7kczslk1xnskls9l2bn1s3dhnjzdzhg8"))))
+                "1z86s8ncl91pxcjnv8fwvgwjjnd384dn5paylwyymrigph4ca4kk"))))
     (properties
      `((upstream-name . "Biostrings")))
     (build-system r-build-system)
@@ -3594,14 +5225,14 @@ biological sequences or sets of sequences.")
 (define-public r-biovizbase
   (package
     (name "r-biovizbase")
-    (version "1.44.0")
+    (version "1.46.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biovizBase" version))
        (sha256
         (base32
-         "1ffzf7yvl47l8v8a50m8g9q33hgwvxg4fcm8ld2yy8hd2zl86zyd"))))
+         "0k56bq3g5vwnd0vkqg7x7v7i9bakwb8s1yl7k5nwj26k4aw96lw6"))))
     (properties `((upstream-name . "biovizBase")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3636,13 +5267,13 @@ effort and encourages consistency.")
 (define-public r-bsgenome
   (package
     (name "r-bsgenome")
-    (version "1.64.0")
+    (version "1.66.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BSgenome" version))
               (sha256
                (base32
-                "17gqrmaf6xxghgrzcansl9gfw3ghkrqp87swlnwgyghqvflr5qxc"))))
+                "0p75c52sw464bdqz7dyda9h8k2wsxdpdxxhya5awh977xaly90pf"))))
     (properties
      `((upstream-name . "BSgenome")))
     (build-system r-build-system)
@@ -3667,14 +5298,14 @@ genome data packages and support for efficient SNP representation.")
 (define-public r-category
   (package
     (name "r-category")
-    (version "2.62.0")
+    (version "2.64.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Category" version))
        (sha256
         (base32
-         "07js03cfdd6gzbzw14iavlqxynfcqszh988v6k1a3h074wxiivqd"))))
+         "1j62b3ycvb27p80k1a1qj4pdf8cjynf5fkj65v74c3l1hgl9qxnh"))))
     (properties `((upstream-name . "Category")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3698,13 +5329,13 @@ analysis.")
 (define-public r-chipseeker
   (package
     (name "r-chipseeker")
-    (version "1.32.0")
+    (version "1.34.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "ChIPseeker" version))
               (sha256
                (base32
-                "001f85nk4myk9vgs05inlj2dfby4802p1iyzkfqg332yk52gsbl7"))))
+                "0jr9mc79di0r3xrc7m27vwk85qa4fpcwp4nb77pr9s6jbv23773r"))))
     (build-system r-build-system)
     (native-inputs
      (list r-knitr))
@@ -3718,6 +5349,7 @@ analysis.")
            r-genomicranges
            r-genomicfeatures
            r-ggplot2
+           r-ggvenndiagram
            r-gplots
            r-gtools
            r-dplyr
@@ -3744,14 +5376,14 @@ annotation, distance to TSS, and overlap of peaks or genes.")
 (define-public r-chipseq
   (package
     (name "r-chipseq")
-    (version "1.46.0")
+    (version "1.48.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "chipseq" version))
        (sha256
         (base32
-         "1vh0hvgnw7ykj401v1q807sl14s4nixp1d8xbm41n01q6w8x834i"))))
+         "1gmspbf5bmlqgbq280lnh4m9bmhzv6d0aj15dmggizsgb9d34vp5"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biocgenerics
@@ -3770,14 +5402,14 @@ experiments.")
 (define-public r-complexheatmap
   (package
     (name "r-complexheatmap")
-    (version "2.12.0")
+    (version "2.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ComplexHeatmap" version))
        (sha256
         (base32
-         "15b49vlkl89prcw70mlw066z0gxhs26x8dpfn6qr3gz7hihygs65"))))
+         "1mf0h2j31m57jd3s1sj8ijn9wdgbg452d79drdkxypxqvpm7b927"))))
     (properties
      `((upstream-name . "ComplexHeatmap")))
     (build-system r-build-system)
@@ -3810,14 +5442,14 @@ self-defined annotation graphics.")
 (define-public r-copywriter
   (package
     (name "r-copywriter")
-    (version "2.28.0")
+    (version "2.29.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "CopywriteR" version))
        (sha256
         (base32
-         "1k11kvam96hpg71hz2n9cfzizmb7d1bmq5zfvm34s7fn09is60xb"))))
+         "1h4cyrjwdazgk49yzi9lvya8bfz9r4cpq19hyzikvc81ia8zdxs6"))))
     (properties `((upstream-name . "CopywriteR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3881,26 +5513,26 @@ distribution.")
 (define-public r-deseq2
   (package
     (name "r-deseq2")
-    (version "1.36.0")
+    (version "1.38.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DESeq2" version))
        (sha256
         (base32
-         "06mvb0jqn2fg96wfwspv0kzpa8xpimzaldrcy8m2d4yk76xwsdr7"))))
+         "1m81yvcl63h5m7kbbxpjk7hzygxmn4l9mlgqrdmnnls56183h3b4"))))
     (properties `((upstream-name . "DESeq2")))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase
            r-biocgenerics
            r-biocparallel
-           r-genefilter
            r-geneplotter
            r-genomicranges
            r-ggplot2
            r-iranges
            r-locfit
+           r-matrixstats
            r-rcpp
            r-rcpparmadillo
            r-s4vectors
@@ -3919,14 +5551,14 @@ distribution.")
 (define-public r-dexseq
   (package
     (name "r-dexseq")
-    (version "1.42.0")
+    (version "1.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DEXSeq" version))
        (sha256
         (base32
-         "1dzx9mvm8pvcrwr88rin3flnpmzp3vq8mvspx9s8virqhv1102am"))))
+         "01728hag1c5fh4n0v57k1p9ss5rqgckab4cnj5flp750myi1fbps"))))
     (properties `((upstream-name . "DEXSeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3964,13 +5596,13 @@ exploration of the results.")
 (define-public r-diffcyt
   (package
     (name "r-diffcyt")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "diffcyt" version))
        (sha256
-        (base32 "0mysylzmg24g7lm1xan4yklzqmskfgh53j6vjcz2gzakz5rq3rdb"))))
+        (base32 "10xhvksnnn4m1hly16fwmbr28xgym6a9zkqj8y476jph4wpnhc2s"))))
     (properties `((upstream-name . "diffcyt")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4002,14 +5634,14 @@ adapted from transcriptomics.")
 (define-public r-dirichletmultinomial
   (package
     (name "r-dirichletmultinomial")
-    (version "1.38.0")
+    (version "1.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DirichletMultinomial" version))
        (sha256
         (base32
-         "15l0h2qz80lmrm5rva3v7lkgddn42igyxxwims57zwpwyhrk9bmx"))))
+         "009nnl3zwcsg6mh7wl3j856dpi7awkyxdy660rqmiskn7m2ah4l1"))))
     (properties
      `((upstream-name . "DirichletMultinomial")))
     (build-system r-build-system)
@@ -4029,13 +5661,13 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2):
 (define-public r-dittoseq
   (package
     (name "r-dittoseq")
-    (version "1.8.1")
+    (version "1.10.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "dittoSeq" version))
               (sha256
                (base32
-                "0vi0hcyffaxp6yxsrq95bdlrhr85dvbqm9c7rg6a6blkfgwhlzb4"))))
+                "0sxpwg2cjw70pzdxbdw68nic521w65ryn83mj0pb2m1ncpimin4b"))))
     (properties `((upstream-name . "dittoSeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4073,14 +5705,14 @@ code{dittoColors()}.")
 (define-public r-edaseq
   (package
     (name "r-edaseq")
-    (version "2.30.0")
+    (version "2.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "EDASeq" version))
        (sha256
         (base32
-         "1qnpbmhxvqsma7ihi6yp3ad962xcanlxald84k2szh011ipxj7ws"))))
+         "0hx4als33lvdchz5s6cv2axvjyp0k8p3v0lm51jayhjcjpmihqzp"))))
     (properties `((upstream-name . "EDASeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4113,13 +5745,13 @@ global-scaling and full-quantile normalization.")
 (define-public r-edger
   (package
     (name "r-edger")
-    (version "3.38.4")
+    (version "3.40.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "edgeR" version))
               (sha256
                (base32
-                "1ww69xrg9qrmq7dix2k48j6akgn58ss3340hm7pjvzx508x1j6n6"))))
+                "1a0rmczlqmqmip2ix28m4iwcpfj04p6nrcl562bjgaifvgyjqhzg"))))
     (properties `((upstream-name . "edgeR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4138,14 +5770,14 @@ CAGE.")
 (define-public r-ensembldb
   (package
     (name "r-ensembldb")
-    (version "2.20.2")
+    (version "2.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ensembldb" version))
        (sha256
         (base32
-         "12n21dcimdhgyjzk33m6xbv0m9ihgyzcf66vr1jr5ycv3rq2s7xc"))))
+         "1v1in3imqbwak3v9w99l6hq8kihai5xvpgxvg7imna7jn1w8kmji"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotationdbi
@@ -4183,14 +5815,14 @@ chromosome region or transcript models of lincRNA genes.")
 (define-public r-fastseg
   (package
     (name "r-fastseg")
-    (version "1.42.0")
+    (version "1.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "fastseg" version))
        (sha256
         (base32
-         "1cr1b1jbgp1z1zpf71kl7mljbm2jpi6b97bf3bll3gnagfm489hy"))))
+         "1m1x7xmbxwa15vzd45h16pnib944f20pwinx1pyhba5hcngkikfi"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase r-biocgenerics r-genomicranges r-iranges
@@ -4210,14 +5842,14 @@ microarrays or GRanges for sequencing data.")
 (define-public r-gage
   (package
     (name "r-gage")
-    (version "2.46.0")
+    (version "2.48.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gage" version))
        (sha256
         (base32
-         "03hx188h98qrbpjlf8v9sg2vqyfv49rp4c18ir11pg6hwqqrxh7b"))))
+         "08qvg1cmrln7w5z33r81kz1zjs8fcj3qbxm1crbsazvb6gdpqyyi"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotationdbi r-go-db r-graph r-keggrest))
@@ -4238,14 +5870,14 @@ analysis using other methods.")
 (define-public r-genefilter
   (package
     (name "r-genefilter")
-    (version "1.78.0")
+    (version "1.80.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "genefilter" version))
        (sha256
         (base32
-         "1lp3alnljhsil8zylf8rvf8ik4wmsyciy3ij4rr9l4191dkkp4aq"))))
+         "0f25z0hqmrkimv14j03pgjsxpq5rz9ymk151rlg4j4vpc06n73cq"))))
     (build-system r-build-system)
     (native-inputs
      (list gfortran r-knitr))
@@ -4262,13 +5894,13 @@ high-throughput sequencing experiments.")
 (define-public r-geneoverlap
   (package
     (name "r-geneoverlap")
-    (version "1.32.0")
+    (version "1.34.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GeneOverlap" version))
               (sha256
                (base32
-                "0nqwa3x9q1hl9nm06hqzzrn00rirc9kj6s320csjlf7x6rcidr93"))))
+                "0ii3ymysqkhyvj204zigpgjny0cglggqmvw311gvgkdi16dib1qs"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-rcolorbrewer r-gplots))
@@ -4281,13 +5913,13 @@ and visualize the results.")
 (define-public r-genomation
   (package
     (name "r-genomation")
-    (version "1.28.0")
+    (version "1.30.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "genomation" version))
               (sha256
                (base32
-                "0rvay7gs4g2wi6h42kln8xwy9b05axj1x8mkfayl6pnnlva6xj79"))))
+                "098ldnh45f48145jfsbdw5dqv5yiqkfci1fy6h6gjz7nh3dvnil5"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biostrings
@@ -4328,13 +5960,13 @@ genomic intervals.  In addition, it can use BAM or BigWig files as input.")
 (define-public r-genomeinfodb
   (package
     (name "r-genomeinfodb")
-    (version "1.32.3")
+    (version "1.34.6")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomeInfoDb" version))
               (sha256
                (base32
-                "17nwcq2ivj3bdibdywfyjq4n6z0djispbh9ahqa55sp31ksq41xh"))))
+                "123kp69fmy5pbqh0j6qxdkvkm4g9pdwzms01i8qnix3m1b9j597w"))))
     (properties
      `((upstream-name . "GenomeInfoDb")))
     (build-system r-build-system)
@@ -4355,13 +5987,13 @@ names in their natural, rather than lexicographic, order.")
 (define-public r-genomicalignments
   (package
     (name "r-genomicalignments")
-    (version "1.32.1")
+    (version "1.34.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicAlignments" version))
               (sha256
                (base32
-                "09pg7822camyav5zvlpv360sj5gz8q1bhk528qa2da2qsz74a3cz"))))
+                "0y9yjyzch0cn2j4yrwfp0z8qw3yqvl8h1dlrl7ylzy9mwsqc6wg5"))))
     (properties
      `((upstream-name . "GenomicAlignments")))
     (build-system r-build-system)
@@ -4388,13 +6020,13 @@ alignments.")
 (define-public r-genomicfeatures
   (package
     (name "r-genomicfeatures")
-    (version "1.48.3")
+    (version "1.50.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicFeatures" version))
               (sha256
                (base32
-                "0f14p1ma2y8l60p9sxmh5j0axws9by1cznczb2jxipphpb4slpl1"))))
+                "14pn7lngayascj5k84g2g748assbivpiakss247cdj9ngzx5sfwz"))))
     (properties
      `((upstream-name . "GenomicFeatures")))
     (build-system r-build-system)
@@ -4432,14 +6064,14 @@ extracting the desired features in a convenient format.")
 (define-public r-genomicfiles
   (package
     (name "r-genomicfiles")
-    (version "1.32.1")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GenomicFiles" version))
        (sha256
         (base32
-         "06ycfna26klx27vvsnlpgv46bymfrc8z0zkpag7nm4m23153ivkz"))))
+         "0k64m9f5y88p90wd87hy0ixj5ly5yi413al9p2bn10b1fjx2c451"))))
     (properties `((upstream-name . "GenomicFiles")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4466,13 +6098,13 @@ provide added flexibility for data combination and manipulation.")
 (define-public r-genomicranges
   (package
     (name "r-genomicranges")
-    (version "1.48.0")
+    (version "1.50.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicRanges" version))
               (sha256
                (base32
-                "088rv1aclwq265pdg4hmks73nl0125vk0vigyi44n3djkrdx48yn"))))
+                "13b6bm6nrxx1vgzrzpf59c2lq5w8kjq9hsch5h037f0p9w3w5z9p"))))
     (properties
      `((upstream-name . "GenomicRanges")))
     (build-system r-build-system)
@@ -4493,14 +6125,14 @@ manipulating genomic intervals and variables defined along a genome.")
 (define-public r-gostats
   (package
     (name "r-gostats")
-    (version "2.62.0")
+    (version "2.64.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GOstats" version))
        (sha256
         (base32
-         "121ly9vifarg8y7mc468571bbs0xv4sx6sflm5zcdqf0p83yvjrm"))))
+         "07chyfkq8nwxjgnlrrwza8jw996dq0ki4bzdfalj9yl1iac1pnys"))))
     (properties `((upstream-name . "GOstats")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4524,14 +6156,14 @@ testing and other simple calculations.")
 (define-public r-gseabase
   (package
     (name "r-gseabase")
-    (version "1.58.0")
+    (version "1.60.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GSEABase" version))
        (sha256
         (base32
-         "1qhvgyg392fd98h2qnmfmhg7mil5hp9cy3qmkqs4x1bhpv1m978g"))))
+         "0i8fliln3v9sw9x34pqafdx1z6jkys8b11fkz4ihmw8lc8lfd0x5"))))
     (properties `((upstream-name . "GSEABase")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4550,17 +6182,44 @@ testing and other simple calculations.")
 Enrichment Analysis} (GSEA).")
     (license license:artistic2.0)))
 
+(define-public r-harshlight
+  (package
+    (name "r-harshlight")
+    (version "1.70.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "Harshlight" version))
+              (sha256
+               (base32
+                "0asjgcnwawg8x7ql0srhb2011rvb4kr2cpsa1cy28nfmjfvdf0qm"))))
+    (properties `((upstream-name . "Harshlight")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-affy
+           r-altcdfenvs
+           r-biobase))
+    (home-page "http://asterion.rockefeller.edu/Harshlight/")
+    (synopsis "Corrective make-up program for microarray chips")
+    (description
+     "The package detects extended diffuse and compact blemishes on microarray
+chips.  Harshlight marks the areas in a collection of chips (affybatch
+objects).  A corrected @code{AffyBatch} object will result.  The package
+replaces the defected areas with @code{N/A}s or the median of the values of
+the same probe.  The new version handles the substitute value as a whole
+matrix to solve the memory problem.")
+    (license license:gpl2+)))
+
 (define-public r-hpar
   (package
     (name "r-hpar")
-    (version "1.38.0")
+    (version "1.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "hpar" version))
        (sha256
         (base32
-         "07c6r703d5xp7y9bqmqalxgna2qrbk1h5s0d992m7360k259mgrj"))))
+         "1dls59d2ysk8ngk5c6nx7xqgc2iygbdlzf88gccf2wm8zhy8m3f4"))))
     (build-system r-build-system)
     (native-inputs
      (list r-knitr))
@@ -4573,14 +6232,14 @@ the Human Protein Atlas project.")
 (define-public r-rhtslib
   (package
     (name "r-rhtslib")
-    (version "1.28.0")
+    (version "2.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rhtslib" version))
        (sha256
         (base32
-         "07kws6afkxbmxq4w357mwwl712pdd16alvz7iqijjd2x7rjchj2f"))))
+         "1ri76wwv44hgxji2bmlqi6v8gbvhr72q0d6nlgpfgfwb9sgvz62h"))))
     (properties `((upstream-name . "Rhtslib")))
     (build-system r-build-system)
     ;; Without this a temporary directory ends up in the Rhtslib.so binary,
@@ -4602,13 +6261,13 @@ of other R packages who wish to make use of HTSlib.")
 (define-public r-impute
   (package
     (name "r-impute")
-    (version "1.70.0")
+    (version "1.72.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "impute" version))
               (sha256
                (base32
-                "11b0z7py0im6y43k55xpzz5jnvc0ram9rk3n1n4mwhvs0vhy39r2"))))
+                "1k697pqlkrwmfszipl9irbzmwhk1vz97j3rh0k5nj2mrj3dr71mv"))))
     (native-inputs
      (list gfortran))
     (build-system r-build-system)
@@ -4622,14 +6281,14 @@ microarray data, using nearest neighbor averaging.")
 (define-public r-interactivedisplaybase
   (package
     (name "r-interactivedisplaybase")
-    (version "1.34.0")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "interactiveDisplayBase" version))
        (sha256
         (base32
-         "0fdwx5ch0ch8axdkfiq7zzhhq5hwcvd6kf8fggw9nd3ah1yjwbdg"))))
+         "1j2cz929q9hwkchnzcs3mnbmhg68mm06r9bgylnbll4j5ibqicrz"))))
     (properties
      `((upstream-name . "interactiveDisplayBase")))
     (build-system r-build-system)
@@ -4647,14 +6306,14 @@ Shiny-based display methods for Bioconductor objects.")
 (define-public r-keggrest
   (package
     (name "r-keggrest")
-    (version "1.36.3")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "KEGGREST" version))
        (sha256
         (base32
-         "0lzb3z6pzm323q70931b7220ygml7jb4g81dybwa79wqiqz15pni"))))
+         "0623p6px259v000pp14c2rknjgivx9c90b626q9bln0qw6wy97zc"))))
     (properties `((upstream-name . "KEGGREST")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4671,13 +6330,13 @@ Shiny-based display methods for Bioconductor objects.")
 (define-public r-lfa
   (package
     (name "r-lfa")
-    (version "1.26.0")
+    (version "1.28.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "lfa" version))
        (sha256
-        (base32 "044866h4fnxmzb3sh9vmrd2smgsbcqgvd19dgwxisi418cad577l"))))
+        (base32 "0047wspvarbnbawrwvfjfz5y6i36l2r2k2501zjya09rjpiq101m"))))
     (properties `((upstream-name . "lfa")))
     (build-system r-build-system)
     (propagated-inputs (list r-corpcor))
@@ -4692,13 +6351,13 @@ Binomial data via estimation of latent structure in the natural parameter.")
 (define-public r-limma
   (package
     (name "r-limma")
-    (version "3.52.2")
+    (version "3.54.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "limma" version))
               (sha256
                (base32
-                "0m8p8pqmf48f2zdf3qs66hmychbc58g2hfg1wyxzsv180m6xkk65"))))
+                "1jy75nbkhl0kgv4gw88acx58r9f1kywrd36405x6g05xy05bprma"))))
     (build-system r-build-system)
     (home-page "http://bioinf.wehi.edu.au/limma")
     (synopsis "Package for linear models for microarray and RNA-seq data")
@@ -4711,13 +6370,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.")
 (define-public r-made4
   (package
     (name "r-made4")
-    (version "1.70.0")
+    (version "1.72.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "made4" version))
               (sha256
                (base32
-                "1wrv9d2mp799qzy1bsaj4w7wx12gdhfv9qvklz7z41vfz59d6bq5"))))
+                "0ylcigzbahic99afqk1q29d4wczmsqmp2hasvihcykybb440a6f2"))))
     (properties `((upstream-name . "made4")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4737,16 +6396,111 @@ reduction (between group analysis) and joint dimension reduction of two
 datasets (coinertia analysis).")
     (license license:artistic2.0)))
 
+(define-public r-makecdfenv
+  (package
+    (name "r-makecdfenv")
+    (version "1.74.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "makecdfenv" version))
+              (sha256
+               (base32
+                "0bvj5dg6yfjnhga1z8788zmb98d8shyz8pzz0ggnml87c1p2gy25"))))
+    (properties `((upstream-name . "makecdfenv")))
+    (build-system r-build-system)
+    (inputs (list zlib))
+    (propagated-inputs
+     (list r-affy
+           r-affyio
+           r-biobase
+           r-zlibbioc))
+    (home-page "https://bioconductor.org/packages/makecdfenv")
+    (synopsis "Chip description file environment maker")
+    (description
+     "This package implements two functions.  One of them reads an Affymetrix
+@acronym{CDF, chip description file} and creates a hash table environment
+containing the location/probe set membership mapping.  The other one creates a
+package that automatically loads that environment.")
+    (license license:gpl2+)))
+
+(define-public r-maser
+  (package
+    (name "r-maser")
+    (version "1.16.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "maser" version))
+              (sha256
+               (base32
+                "1zycx8s046g4d3w5qrn950bmi0nrnq1g7fvqji48mr6hmsyzplvv"))))
+    (properties `((upstream-name . "maser")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biocgenerics
+           r-data-table
+           r-dplyr
+           r-dt
+           r-genomeinfodb
+           r-genomicranges
+           r-ggplot2
+           r-gviz
+           r-iranges
+           r-reshape2
+           r-rtracklayer))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/DiogoVeiga/maser")
+    (synopsis "Mapping alternative splicing events to proteins")
+    (description
+     "This package provides functionalities for downstream analysis, annotation
+and visualizaton of alternative splicing events generated by rMATS.")
+    (license license:expat)))
+
+(define-public r-metaneighbor
+  (package
+    (name "r-metaneighbor")
+    (version "1.18.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "MetaNeighbor" version))
+              (sha256
+               (base32
+                "1gjjp5qlmv26sd3fvrd8cgv3invckxr8ldjpizpqm4mxjzifxwpm"))))
+    (properties `((upstream-name . "MetaNeighbor")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-beanplot
+           r-dplyr
+           r-ggplot2
+           r-gplots
+           r-igraph
+           r-matrix
+           r-matrixstats
+           r-rcolorbrewer
+           r-singlecellexperiment
+           r-summarizedexperiment
+           r-tibble
+           r-tidyr))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/MetaNeighbor")
+    (synopsis "Single cell replicability analysis")
+    (description
+     "This package implements a method to rapidly assess cell type identity using
+both functional and random gene sets and it allows users to quantify cell type
+replicability across datasets using neighbor voting.  @code{MetaNeighbor} works
+on the basis that cells of the same type should have more similar gene expression
+profiles than cells of different types.")
+    (license license:expat)))
+
 (define-public r-methylkit
   (package
     (name "r-methylkit")
-    (version "1.22.0")
+    (version "1.24.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "methylKit" version))
               (sha256
                (base32
-                "00asjzv05avfg0rrkmfbdqd6xx8d18zi72n3b1kf9wj81z2d2a35"))))
+                "0w6wv8x1jggbvymb07b2z47myf239mwpwbgz5p5yi60qb0k7p2q9"))))
     (properties `((upstream-name . "methylKit")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4814,14 +6568,14 @@ throughput genetic sequencing data sets using regression methods.")
 (define-public r-muscat
   (package
     (name "r-muscat")
-    (version "1.10.1")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "muscat" version))
        (sha256
         (base32
-         "1j3zkhqgza92vdykb1yia1jjwsdqra6q9c0jk6p5p2x0778xqgfd"))))
+         "07b1z8rd0zibmv3rm4zggjf49lh37p2bp1h919zcw3n0fy2hax1k"))))
     (properties `((upstream-name . "muscat")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4864,14 +6618,14 @@ platform that mimics both single and multi-sample scRNA-seq data.")
 (define-public r-mutationalpatterns
   (package
     (name "r-mutationalpatterns")
-    (version "3.6.0")
+    (version "3.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MutationalPatterns" version))
        (sha256
         (base32
-         "113b2hrc0n47qz144xhky93jcm6qh6flzadq5y0plga5jrz0rnwg"))))
+         "071s1hfxln8zdr303g0ifmajd3kcfxxb6dds0pz67chc2gmgnd9q"))))
     (build-system r-build-system)
     (native-inputs
      (list r-knitr))
@@ -4910,14 +6664,14 @@ in SNV base substitution data.")
 (define-public r-msnbase
   (package
     (name "r-msnbase")
-    (version "2.22.0")
+    (version "2.24.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MSnbase" version))
        (sha256
         (base32
-         "1xzn0k3c2wn6c6gv90hddy3c201sg927342zrw9ig2xap0r053x3"))))
+         "0jdq41rhn9qyhxfihvrgim76fzdrycc02wjsjdrff42gmray49w7"))))
     (properties `((upstream-name . "MSnbase")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4955,14 +6709,14 @@ of mass spectrometry based proteomics data.")
 (define-public r-msnid
   (package
     (name "r-msnid")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MSnID" version))
        (sha256
         (base32
-         "1yiw95p40nz0pvq7s4i0xg02r9yqmnknak00z4lkw8jij3w3rkkq"))))
+         "1ljhxbyq5pa32sh44f06cwcdq79xh5nm51bpx1i8xig3bvwyg7p9"))))
     (properties `((upstream-name . "MSnID")))
     (build-system r-build-system)
     (arguments
@@ -5012,14 +6766,14 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.")
 (define-public r-mzid
   (package
     (name "r-mzid")
-    (version "1.34.0")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "mzID" version))
        (sha256
         (base32
-         "1q1aqyya9nd494s7m3rdaf3kixipdrwbj825g40kdljwrg85y961"))))
+         "0h5w5ykbziaif6m61pa5x92f2rblfgldvj9vajfhkmxj1b2ks9za"))))
     (properties `((upstream-name . "mzID")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5043,14 +6797,14 @@ specific parser.")
 (define-public r-mzr
   (package
     (name "r-mzr")
-    (version "2.30.0")
+    (version "2.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "mzR" version))
        (sha256
         (base32
-         "1dqa03hb42kbqfg15ksijdkyf9pr54gcl3in4mzjkld5sdi8ncds"))
+         "0p7mkvvaf25si95lpwpr65jm3dzxmgs9i0wilyb2mbxkdcz9vm71"))
        (modules '((guix build utils)))
        (snippet
         '(delete-file-recursively "src/boost"))))
@@ -5091,17 +6845,84 @@ proteowizard library for mzML and mzIdentML.  The netCDF reading code has
 previously been used in XCMS.")
     (license license:artistic2.0)))
 
+;; This is a CRAN package, but it depends on a Bioconductor package.
+(define-public r-numbat
+  (package
+    (name "r-numbat")
+    (version "1.2.1")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "numbat" version))
+              (sha256
+               (base32
+                "1jkz24j99cd333mvisp8x5swwr0iyix1kc962d2yx3mv5cn28xdb"))))
+    (properties `((upstream-name . "numbat")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-ape
+                             r-catools
+                             r-data-table
+                             r-dendextend
+                             r-dplyr
+                             r-genomicranges
+                             r-ggplot2
+                             r-ggraph
+                             r-ggtree
+                             r-glue
+                             r-igraph
+                             r-iranges
+                             r-logger
+                             r-magrittr
+                             r-matrix
+                             r-optparse
+                             r-paralleldist
+                             r-patchwork
+                             r-pryr
+                             r-purrr
+                             r-r-utils
+                             r-rcpp
+                             r-rcpparmadillo
+                             r-rhpcblasctl
+                             r-roptim
+                             r-scales
+                             r-scistreer
+                             r-stringr
+                             r-tibble
+                             r-tidygraph
+                             r-tidyr
+                             r-vcfr
+                             r-zoo))
+    (home-page "https://github.com/kharchenkolab/numbat")
+    (synopsis "Haplotype-aware CNV analysis from scRNA-Seq")
+    (description
+     "This package provides a computational method that infers copy number
+variations (CNV) in cancer scRNA-seq data and reconstructs the tumor
+phylogeny.  It integrates signals from gene expression, allelic ratio, and
+population haplotype structures to accurately infer allele-specific CNVs in
+single cells and reconstruct their lineage relationship.  It does not require
+tumor/normal-paired DNA or genotype data, but operates solely on the donor
+scRNA-data data (for example, 10x Cell Ranger output).  It can be used to:
+
+@enumerate
+@item detect allele-specific copy number variations from single-cells
+@item differentiate tumor versus normal cells in the tumor microenvironment
+@item infer the clonal architecture and evolutionary history of profiled tumors
+@end enumerate
+
+For details on the method see @url{https://doi.org/10.1038/s41587-022-01468-y,
+Gao et al in Nature Biotechnology 2022}.")
+    (license license:expat)))
+
 (define-public r-organism-dplyr
   (package
     (name "r-organism-dplyr")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Organism.dplyr" version))
        (sha256
         (base32
-         "0j29f85d66c45ww3417xx376vpz0mmvga5n7h2cl1sd4h70b55as"))))
+         "1hawn8pp63kal5ml0sm3h1j1wnkq02z64sliyaf6apv7vl60ja9g"))))
     (properties `((upstream-name . "Organism.dplyr")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5133,14 +6954,14 @@ functionality of the @code{TxDb} packages (e.g.,
 (define-public r-organismdbi
   (package
     (name "r-organismdbi")
-    (version "1.38.1")
+    (version "1.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "OrganismDbi" version))
        (sha256
         (base32
-         "0mxnxj8x4hc21psz39mf7qwvh1fsn6qyjgl5qffk1xxmasf69619"))))
+         "11l1xqwbqs129vxd6lxdaizpp6j08spyh6799rv5wqmlymap1ykw"))))
     (properties `((upstream-name . "OrganismDbi")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5165,14 +6986,14 @@ the fact that each of these packages implements a select methods.")
 (define-public r-pcaexplorer
   (package
     (name "r-pcaexplorer")
-    (version "2.22.0")
+    (version "2.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "pcaExplorer" version))
        (sha256
         (base32
-         "0xkafpi6y5n8hljdaj183hd5z4ik7lpbklg2cbx1hwfz4n4hh1bl"))))
+         "0gs4az4h5mwnr3s8fq7im5p3mm4mhc0x5amjr2badqkw1fih3jp7"))))
     (properties `((upstream-name . "pcaExplorer")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5220,14 +7041,14 @@ application encapsulates the whole analysis.")
 (define-public r-pcamethods
   (package
     (name "r-pcamethods")
-    (version "1.88.0")
+    (version "1.90.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "pcaMethods" version))
        (sha256
         (base32
-         "1087sl7y707zld7zpf3ly51gnmdp93vn90dwa5440v7qawvg2h9b"))))
+         "1cjmkfpbbfzkx6bi3r9jjx54iwkm4gl8hqa1776hxicq2x2c83s4"))))
     (properties `((upstream-name . "pcaMethods")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5289,14 +7110,14 @@ chromosome.  Both tumor-normal paired and tumor-only analyses are supported.")
 (define-public r-protgenerics
   (package
     (name "r-protgenerics")
-    (version "1.28.0")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ProtGenerics" version))
        (sha256
         (base32
-         "04hcgj4q8dbzp1a29rbww2bxxrg679pgys3m09p0ydkpsx76rq05"))))
+         "1k5pg0zbhz9mjsl5i3j33p7qv2adax2lf7yqv6qz229fxxaxs5li"))))
     (properties `((upstream-name . "ProtGenerics")))
     (build-system r-build-system)
     (home-page "https://github.com/lgatto/ProtGenerics")
@@ -5309,14 +7130,14 @@ proteomics packages.")
 (define-public r-rbgl
   (package
     (name "r-rbgl")
-    (version "1.72.0")
+    (version "1.74.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RBGL" version))
        (sha256
         (base32
-         "0ph089vxla49sng0pdwiyh9rpk9i96cbsx5q2jn46jj4x51ijc7y"))))
+         "0dccxsynfnhjzjk22hr5kg068zbg33g6kyhlhlhqh78582181j9m"))))
     (properties `((upstream-name . "RBGL")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5331,13 +7152,13 @@ the graph algorithms contained in the Boost library.")
 (define-public r-rcas
   (package
     (name "r-rcas")
-    (version "1.22.0")
+    (version "1.24.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "RCAS" version))
               (sha256
                (base32
-                "05sj2ab7bxgf41gkmjaskhqm0198xlir1sw3f73x8rjg14rssmqf"))))
+                "0wja7m3b3zr0m8nwcq5m5appsr09jdwkvvvxzh2r5mhksn0abs6p"))))
     (properties `((upstream-name . "RCAS")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5381,14 +7202,14 @@ library implementing most of the pipeline's features.")
 (define-public r-regioner
   (package
     (name "r-regioner")
-    (version "1.28.0")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "regioneR" version))
        (sha256
         (base32
-         "11whi2v211xiz9s7cjl14d8vavlry2fmhvx12rma25wkjmhrpa3f"))))
+         "01anwhz0axdl0g2zsaqz1qdxswxrryarbw6pmn5kmlpz4ipiq049"))))
     (properties `((upstream-name . "regioneR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5412,14 +7233,14 @@ region sets and other genomic features.")
 (define-public r-reportingtools
   (package
     (name "r-reportingtools")
-    (version "2.36.0")
+    (version "2.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ReportingTools" version))
        (sha256
         (base32
-         "0r8cdqzfh1jxkghhk3j8x3y9kkmdyg9ibfhsic15jqkmp1im6khh"))))
+         "1nrgnb002qv0yzmrvg59i9b5wzxda0fdkrmdi6vr15g0g7j3yry0"))))
     (properties
      `((upstream-name . "ReportingTools")))
     (build-system r-build-system)
@@ -5462,13 +7283,13 @@ browser.")
 (define-public r-rhdf5
   (package
     (name "r-rhdf5")
-    (version "2.40.0")
+    (version "2.42.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "rhdf5" version))
               (sha256
                (base32
-                "00cp90mnb8p83jiflm6x4x0qf4p7gvgh47jk9jry6j3qyvfqaiff"))))
+                "1vxs227d1295fz8irr6fsv603cw96a801j8njhblvs0cry38d087"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-rhdf5filters r-rhdf5lib))
@@ -5489,14 +7310,14 @@ the available RAM.")
 (define-public r-rhdf5filters
   (package
     (name "r-rhdf5filters")
-    (version "1.8.0")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "rhdf5filters" version))
        (sha256
         (base32
-         "1ipg0v8nqz1imj63scqmpiswcxbl4ankg3knfq4p06ic6ypbbmvs"))))
+         "17x2a3122mm3z9qnalw25am2x08cfpm17nwhigabid3ha3d2mgz1"))))
     (properties `((upstream-name . "rhdf5filters")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5515,13 +7336,13 @@ HDF5 datasets.")
 (define-public r-rsamtools
   (package
     (name "r-rsamtools")
-    (version "2.12.0")
+    (version "2.14.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Rsamtools" version))
               (sha256
                (base32
-                "1wll703if12qrn0d11ljwf7rqhs4lb27fzyyz1hqwvzn3v361s10"))))
+                "0wd4hsn19msz0fkwfq7gvi97vlfpsbzzw3rjj4b6z7s5a83zir2z"))))
     (properties
      `((upstream-name . "Rsamtools")))
     (build-system r-build-system)
@@ -5580,13 +7401,13 @@ tab-delimited (tabix) files.")
 (define-public r-rtracklayer
   (package
     (name "r-rtracklayer")
-    (version "1.56.1")
+    (version "1.58.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "rtracklayer" version))
               (sha256
                (base32
-                "10qy9s6253mgj871qfqn03i8yw10mz7id4cxfyf67qxczz2xmjls"))))
+                "1qxr0ffmmkbfkbijz7pbks3kvms9k4a5rmma4j9p7ar477fxvlmk"))))
     (build-system r-build-system)
     (arguments
      `(#:phases
@@ -5659,13 +7480,13 @@ differential expression analysis, RNAseq data and related problems.")
 (define-public r-scannotatr
   (package
     (name "r-scannotatr")
-    (version "1.2.0")
+    (version "1.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scAnnotatR" version))
        (sha256
-        (base32 "067q57kabhqd1z8l3d91fw74aaw89nb48gm6fll4hv00nqza3n5b"))))
+        (base32 "0rc035kzbzrxvlcpphzg0yg7q82jvlxpi9xjq8q59hvbpyg1sz93"))))
     (properties `((upstream-name . "scAnnotatR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5696,13 +7517,13 @@ cell types based on specific research needs.")
 (define-public r-scdblfinder
   (package
     (name "r-scdblfinder")
-    (version "1.10.0")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scDblFinder" version))
        (sha256
-        (base32 "0y14dvdm16b3bvlrnz03adfylm1kj6jrp2fwciyldij2lfal90y0"))))
+        (base32 "0gslh28rycx0p6a6fmzbsqy1hg2sn3pp5blxgw01qk9f0ank7szi"))))
     (properties `((upstream-name . "scDblFinder")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5738,16 +7559,53 @@ includes methods formerly found in the scran package, and the new fast and
 comprehensive scDblFinder method.")
     (license license:gpl3)))
 
+;; This is a CRAN package, but it depends on packages from Bioconductor.
+(define-public r-scistreer
+  (package
+    (name "r-scistreer")
+    (version "1.1.0")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "scistreer" version))
+              (sha256
+               (base32
+                "0cdp26ngfp5rxa21nqnj6j2098f6996368g4msb3shh7n75np4s9"))))
+    (properties `((upstream-name . "scistreer")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-ape
+                             r-dplyr
+                             r-ggplot2
+                             r-ggtree
+                             r-igraph
+                             r-paralleldist
+                             r-patchwork
+                             r-phangorn
+                             r-rcpp
+                             r-rcpparmadillo
+                             r-rcppparallel
+                             r-reshape2
+                             r-rhpcblasctl
+                             r-stringr
+                             r-tidygraph))
+    (home-page "https://github.com/kharchenkolab/scistreer")
+    (synopsis "Maximum-likelihood perfect phylogeny Inference at scale")
+    (description
+     "This package provides fast maximum-likelihood phylogeny inference from
+noisy single-cell data using the ScisTree algorithm proposed by
+@code{doi.org/10.1093/bioinformatics/btz676, Yufeng Wu (2019)}.  It makes the
+method applicable to massive single-cell datasets (>10,000 cells).")
+    (license license:gpl3)))
+
 (define-public r-scmap
   (package
     (name "r-scmap")
-    (version "1.18.0")
+    (version "1.20.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scmap" version))
        (sha256
-        (base32 "0pfwaa9pgml11b84rpf7afdkmg8kxb4srgpc56571vaz388xrv7l"))))
+        (base32 "0rq185ynk874vgw4a5s2n92381dj6kxxnx2fcx2v7b2ahr3ybys7"))))
     (properties `((upstream-name . "scmap")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5783,13 +7641,13 @@ different experiment.")
 (define-public r-scry
   (package
     (name "r-scry")
-    (version "1.8.0")
+    (version "1.10.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "scry" version))
               (sha256
                (base32
-                "16mj21r91jy8ircdz8rfrdli9gjy0hrx90kf6ghs305d3d4dl193"))))
+                "0vx6fi8hnxms6d3hm3qxkrdx1qpyd7vhwdk7ds98ads070miqr21"))))
     (properties `((upstream-name . "scry")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5815,14 +7673,14 @@ single-cell RNA-seq.")
 (define-public r-seqlogo
   (package
     (name "r-seqlogo")
-    (version "1.62.0")
+    (version "1.64.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "seqLogo" version))
        (sha256
         (base32
-         "1lk3238m17acmd6lgjjbpscyxw8fm63wv34kbbr478wcih1wbwxr"))))
+         "1xlxi1iaqj7iabzbx15j6pk4551dyj6pa6a6qf5ffr3v7k2pmznp"))))
     (properties `((upstream-name . "seqLogo")))
     (build-system r-build-system)
     (native-inputs
@@ -5838,13 +7696,13 @@ Stephens (1990).")
 (define-public r-seqpattern
   (package
     (name "r-seqpattern")
-    (version "1.28.0")
+    (version "1.30.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "seqPattern" version))
               (sha256
                (base32
-                "0nrrlr1nl9zxmp88qq8jn7wgmda6jh0xvp4nph94w4nwjsyb7xqn"))))
+                "17nvxy8kdc1k0kyf0qny6jp3gzr024q37mmh5x18jjr794hnf9s5"))))
     (properties
      `((upstream-name . "seqPattern")))
     (build-system r-build-system)
@@ -5861,14 +7719,14 @@ reference point and sorted by a user defined feature.")
 (define-public r-shortread
   (package
     (name "r-shortread")
-    (version "1.54.0")
+    (version "1.56.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ShortRead" version))
        (sha256
         (base32
-         "0303198b4v2wjah9kc829kn01030996l6di4jpf8q5ccd212rjhq"))))
+         "1dvnjjc6cwn9wicki3ff3w3zx7i0szj0lnfw4n6lbmipg4ia5bkb"))))
     (properties `((upstream-name . "ShortRead")))
     (build-system r-build-system)
     (inputs
@@ -5904,14 +7762,14 @@ ungapped alignment formats.")
 (define-public r-simplifyenrichment
   (package
     (name "r-simplifyenrichment")
-    (version "1.6.1")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "simplifyEnrichment" version))
        (sha256
         (base32
-         "0qblgdxmr7zc981529cca3ykakql618q1im6gaxw8pwws5jgpyk6"))))
+         "130x5hy6jzglc6clwanh2kmhw567i802w620ffs3977kjfpjsjgy"))))
     (properties
      `((upstream-name . "simplifyEnrichment")))
     (build-system r-build-system)
@@ -5945,13 +7803,13 @@ and comparing the clusterings.")
 (define-public r-transcriptr
   (package
     (name "r-transcriptr")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "transcriptR" version))
        (sha256
-        (base32 "1zc6aasd5nzwl9jxr0rdriiq85adqdbfi5b9m3jyf69pa71sgy03"))))
+        (base32 "03v8xn777vyma82ma5dzk07i1g7406cvsybdz4bf6hj8bgx5ynw7"))))
     (properties `((upstream-name . "transcriptR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5995,14 +7853,14 @@ able to deal also with novel and case specific events.")
 (define-public r-trajectoryutils
   (package
     (name "r-trajectoryutils")
-    (version "1.4.0")
+    (version "1.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "TrajectoryUtils" version))
        (sha256
         (base32
-         "07hcr3zplxlzlwc13wh9006m5kaqm57cm1b2x74bpp857f2q93dj"))))
+         "130w4vpsmrkg458n3wbhvlchg171gjqybvs2w14bxa608f3fzw03"))))
     (properties
      `((upstream-name . "TrajectoryUtils")))
     (build-system r-build-system)
@@ -6019,16 +7877,44 @@ includes a function to create a cluster-level minimum spanning tree and data
 structures to hold pseudotime inference results.")
     (license license:gpl3)))
 
+(define-public r-scds
+  (package
+    (name "r-scds")
+    (version "1.14.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "scds" version))
+              (sha256
+               (base32
+                "0zdf9yf5s0l8ma7d8yhi7bjd964yj84f5h6aq2p0sypjlnc515hd"))))
+    (properties `((upstream-name . "scds")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-dplyr
+                             r-matrix
+                             r-proc
+                             r-s4vectors
+                             r-singlecellexperiment
+                             r-summarizedexperiment
+                             r-xgboost))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/scds")
+    (synopsis "In-silico doublet annotation for single cell RNA sequencing data")
+    (description
+     "This is an R package for doublet annotation of single cell RNA
+sequencing data.  @code{scds} provides methods to annotate doublets in
+scRNA-seq data computationally.")
+    (license license:expat)))
+
 (define-public r-slingshot
   (package
    (name "r-slingshot")
-   (version "2.4.0")
+   (version "2.6.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "slingshot" version))
             (sha256
              (base32
-              "0xapi66l5z2qdqns3fcjqcjal6npqj7rxra60lwjvbrq49pq69p2"))))
+              "00h9iid2z9r55l4hlaa1q0nkbcfq0f7k2afkw4ymjwhm1b8yqj33"))))
    (build-system r-build-system)
    (propagated-inputs
     (list r-igraph
@@ -6051,16 +7937,56 @@ events and allows for the incorporation of prior knowledge through supervised
 graph construction.")
    (license license:artistic2.0)))
 
+;; This is a CRAN package but it depends on a bioconductor package.
+(define-public r-speaq
+  (package
+    (name "r-speaq")
+    (version "2.7.0")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "speaq" version))
+              (sha256
+               (base32
+                "0z9a3nbfazphp090c6hg892vjq7jp4g4cij3s5wbs1q567inbmlk"))))
+    (properties `((upstream-name . "speaq")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-cluster
+           r-data-table
+           r-dosnow
+           r-foreach
+           r-ggplot2
+           r-gridextra
+           r-impute
+           r-massspecwavelet
+           r-missforest
+           r-reshape2
+           r-rfast
+           r-rvest
+           r-xml2))
+    (native-inputs (list r-knitr))
+    (home-page "https://cran.r-project.org/package=speaq")
+    (synopsis "Tools for nuclear magnetic resonance spectra alignment")
+    (description
+     "This package aims to make @acronym{NMR, Nuclear Magnetic Resonance}
+spectroscopy data analysis as easy as possible.  It only requires a small set
+of functions to perform an entire analysis.  Speaq offers the possibility of
+raw spectra alignment and quantitation but also an analysis based on features
+whereby the spectra are converted to peaks which are then grouped and turned
+into features.  These features can be processed with any number of statistical
+tools either included in speaq or available elsewhere on CRAN.")
+    (license license:asl2.0)))
+
 (define-public r-stager
   (package
     (name "r-stager")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "stageR" version))
        (sha256
-        (base32 "0ns3ih6l4na6irshrc5iy4d9qf7hrnqq3ndnlcjb2i1cn38l2w9y"))))
+        (base32 "1layvv9akzijw2br9jzw6cwxn2rimha4m48fm8wn465n1nqcns0m"))))
     (properties `((upstream-name . "stageR")))
     (build-system r-build-system)
     (propagated-inputs (list r-summarizedexperiment))
@@ -6077,13 +8003,13 @@ Biology at
 (define-public r-stringdb
   (package
     (name "r-stringdb")
-    (version "2.8.4")
+    (version "2.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "STRINGdb" version))
        (sha256
-        (base32 "1jn6080v6097zpqsr4gfbx31gqqdhpzjrk63avk3v3xwawmf2379"))))
+        (base32 "1md79vx4270wgh07g3m1mypdki1b9d4a558zxplcalwppqh0dsmp"))))
     (properties `((upstream-name . "STRINGdb")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6110,13 +8036,13 @@ that integrates the various evidences.")
 (define-public r-structuralvariantannotation
   (package
     (name "r-structuralvariantannotation")
-    (version "1.12.0")
+    (version "1.13.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "StructuralVariantAnnotation" version))
        (sha256
-        (base32 "0f3x74ic3blg8nm5xlv79k0n8j3fpl98mmhfanqfzmdl0g3j6wx6"))))
+        (base32 "11z3acsbaifrxkghd7i8503ki9s1lc6c22880yna6qcfprlzb44g"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-assertthat
@@ -6147,13 +8073,13 @@ involving two separate genomic loci encoded as GRanges objects.")
 (define-public r-summarizedexperiment
   (package
     (name "r-summarizedexperiment")
-    (version "1.26.1")
+    (version "1.28.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "SummarizedExperiment" version))
               (sha256
                (base32
-                "02vlqzmslyijs09jl0gdjxqjjnnl4yqbqqqlb4vb7nr0fspmyz39"))))
+                "0897v6x1ki4m7kajnd60yv5qj6xa1293sj572b4dhcnfjvsf9rcn"))))
     (properties
      `((upstream-name . "SummarizedExperiment")))
     (build-system r-build-system)
@@ -6181,14 +8107,14 @@ samples.")
 (define-public r-sva
   (package
     (name "r-sva")
-    (version "3.44.0")
+    (version "3.46.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "sva" version))
        (sha256
         (base32
-         "0ka259rn0la0hjslj7w24q1dyyh79h84nw6mxp7armqbfjb207a4"))))
+         "0c1b7w4rvyy8i0jygj8g9xgf46rmgx8bpdlp2x4fdjr9xsrsl23g"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-edger
@@ -6212,14 +8138,14 @@ unmodeled, or latent sources of noise.")
 (define-public r-systempiper
   (package
     (name "r-systempiper")
-    (version "2.2.2")
+    (version "2.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "systemPipeR" version))
        (sha256
         (base32
-         "1yybbff29gwv6rm0nw4yjw73bbl5prfj8gj4zky917smjfd459im"))))
+         "0lwc4d4k6qmnwsh8fpp5rmiaxhzwl2f0dhzs23ska5xy04466r49"))))
     (properties `((upstream-name . "systemPipeR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6255,13 +8181,13 @@ annotation infrastructure.")
 (define-public r-topgo
   (package
     (name "r-topgo")
-    (version "2.48.0")
+    (version "2.50.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "topGO" version))
               (sha256
                (base32
-                "125r42ymk1irjmwk4sywjkcshs71s26p3zsvryfdvf56k5w162v6"))))
+                "1ripdn7mcabh96bm4p807dbwj7jv05a54kss4snhz84svqq383m4"))))
     (properties
      `((upstream-name . "topGO")))
     (build-system r-build-system)
@@ -6288,13 +8214,13 @@ dependencies between GO terms can be implemented and applied.")
 (define-public r-tximport
   (package
     (name "r-tximport")
-    (version "1.24.0")
+    (version "1.26.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "tximport" version))
               (sha256
                (base32
-                "1cnra82pvwz79a1hkw0phc6aa3v43r5p4nx8xyx5wzmkd7rjkc8x"))))
+                "1r67q4nb2bx9nqycyr2gnfmh4gizl0c7l510vmlcdvplv3yi73yn"))))
     (build-system r-build-system)
     (native-inputs
      (list r-knitr))
@@ -6313,17 +8239,18 @@ of gene-level counts.")
 (define-public r-valr
   (package
     (name "r-valr")
-    (version "0.6.5")
+    (version "0.6.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "valr" version))
        (sha256
         (base32
-         "1674sqclgi4l5r544pjjsblzl1ix2cy961jpkncb3ym47y6c1msw"))))
+         "0w3j8fkssp9s4ybaw8hvqbmsh5m991xkgr4nji3zar2pgmgk3qph"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-broom
+           r-cli
            r-dplyr
            r-ggplot2
            r-rcpp
@@ -6345,13 +8272,13 @@ R, enabling interactive analysis and visualization of genome-scale data.")
 (define-public r-variantannotation
   (package
     (name "r-variantannotation")
-    (version "1.42.1")
+    (version "1.44.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "VariantAnnotation" version))
               (sha256
                (base32
-                "12d5hkx6pby6l2asyg4jp4jb2x17ybwhqd55rl64h37mwcndbdg1"))))
+                "08rm27jcx6amawqdh59291r0qzkr5cdhbhm0xbjbd5mvdpp1icl8"))))
     (properties
      `((upstream-name . "VariantAnnotation")))
     (propagated-inputs
@@ -6383,14 +8310,14 @@ coding changes and predict coding outcomes.")
 (define-public r-vsn
   (package
     (name "r-vsn")
-    (version "3.64.0")
+    (version "3.66.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "vsn" version))
        (sha256
         (base32
-         "1ja7vdjvgx671l57f9fzfn4vc6q7xzfmqs4krg2rdyfaaf531gqf"))))
+         "1k77rg5jf646m1pn59qhlsbb9fzhlpnrj4dzxagknawcbpnnjl0z"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-affy r-biobase r-ggplot2 r-lattice r-limma))
@@ -6452,13 +8379,13 @@ inference.")
 (define-public r-xina
   (package
     (name "r-xina")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "XINA" version))
        (sha256
-        (base32 "03gf7mqpnwx12kny9fsaskgrw83b0wi2cf1j4dbq46pfxjx34v1g"))))
+        (base32 "1c97lsb5shixh4n4mi9kh4gz4qnia9vq736rnzxbs03n5bvlmwlq"))))
     (properties `((upstream-name . "XINA")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6488,13 +8415,13 @@ molecular functions, respectively, and produces intuitive graphical outputs.")
 (define-public r-xmapbridge
   (package
     (name "r-xmapbridge")
-    (version "1.54.0")
+    (version "1.56.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "xmapbridge" version))
        (sha256
-        (base32 "1n3nxc4jwxf5z32i70sza52nyk29adhp8vc3hac7r5b8mbi6gg10"))))
+        (base32 "0wxr3db2daj4xlr9df6iqwm00m71kln7rhqnq2ckdsricblanhs7"))))
     (properties `((upstream-name . "xmapbridge")))
     (build-system r-build-system)
     (home-page "https://git.bioconductor.org/packages/xmapbridge")
@@ -6515,13 +8442,13 @@ describing each of the graphs.")
 (define-public r-xvector
   (package
     (name "r-xvector")
-    (version "0.36.0")
+    (version "0.38.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "XVector" version))
               (sha256
                (base32
-                "1f3sbqy279gb9k13l73j00ixywa1havlqy81zx766r1xkz15nvhk"))))
+                "0ygdyh3s4qsaay930a5lbnmgh6a4gqp5ck9ww466yk0jyk1hxfp9"))))
     (properties
      `((upstream-name . "XVector")))
     (build-system r-build-system)
@@ -6549,13 +8476,13 @@ describing each of the graphs.")
 (define-public r-zlibbioc
   (package
     (name "r-zlibbioc")
-    (version "1.42.0")
+    (version "1.44.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "zlibbioc" version))
               (sha256
                (base32
-                "0w0y9jixdk6akmasn55g9g0nhlh93hbca5bwx5w1fypnvqrqpxzv"))))
+                "0c75mf0iw6bgwrn3zxpz1dz03aw7p6a1mfhssk6i1mp24avic9lb"))))
     (properties
      `((upstream-name . "zlibbioc")))
     (build-system r-build-system)
@@ -6568,13 +8495,13 @@ libraries for systems that do not have these available via other means.")
 (define-public r-zellkonverter
   (package
     (name "r-zellkonverter")
-    (version "1.6.3")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "zellkonverter" version))
        (sha256
-        (base32 "0l6v7a2zyxpq2w3vm85z439ldi3ld3pkc3wx95a1vxzbr31cpdzz"))))
+        (base32 "0b14v6lyhfapmfj8j729k5cmgxc4df6wsk2rds0q4y6z4hiwgmxy"))))
     (properties `((upstream-name . "zellkonverter")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6600,14 +8527,14 @@ saving AnnData objects to disk.")
 (define-public r-geneplotter
   (package
     (name "r-geneplotter")
-    (version "1.74.0")
+    (version "1.76.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "geneplotter" version))
        (sha256
         (base32
-         "13230mzrdralnvf9jp032s16a8mk3kx5476nnvpa4pvcgp1i1ijc"))))
+         "094v4skdvsnc7bp3acj801ih022w9k96f2b857326vd19khz0ava"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotate
@@ -6625,14 +8552,14 @@ saving AnnData objects to disk.")
 (define-public r-oligoclasses
   (package
     (name "r-oligoclasses")
-    (version "1.58.0")
+    (version "1.60.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "oligoClasses" version))
        (sha256
         (base32
-         "1m4x50gl1fm5waa531v7ml0q229q65qn9cgiwnvjg721fvra7mdk"))))
+         "1ik9xfx6g4gf54hm5f5prip1iz6694czpbhlgwd3p9qh8ddndgp8"))))
     (properties `((upstream-name . "oligoClasses")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6660,14 +8587,14 @@ packages.")
 (define-public r-oligo
   (package
     (name "r-oligo")
-    (version "1.60.0")
+    (version "1.62.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "oligo" version))
        (sha256
         (base32
-         "0y7j96rafm9b85sxq2483i73685i3j67lk33fn8nfcav6lmsv5vy"))))
+         "1rhzav57d092ip9qjsmskj3l8h4xyq8cpa2a2jl8g32fwh0dyvsz"))))
     (properties `((upstream-name . "oligo")))
     (build-system r-build-system)
     (inputs (list zlib))
@@ -6696,14 +8623,14 @@ Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
 (define-public r-qvalue
   (package
     (name "r-qvalue")
-    (version "2.28.0")
+    (version "2.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "qvalue" version))
        (sha256
         (base32
-         "0cvhm5cldcnnxwa293dig1pj9lvj2hnz9zh4gfr25sw0xlcjzmyw"))))
+         "1dsia1c9ir989aqrgl5j5v4bysm3pyw9225yrcajiwgl8fxymph4"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-ggplot2 r-reshape2))
@@ -6751,13 +8678,13 @@ problems in genomics, brain imaging, astrophysics, and data mining.")
 (define-public r-apeglm
   (package
    (name "r-apeglm")
-   (version "1.18.0")
+   (version "1.20.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "apeglm" version))
             (sha256
              (base32
-              "1ppwk4g66x46hpqsfsvhl12398d1srqr47nmp0y2gz212kff0rby"))))
+              "1hk2y7r734wdd56f18l03kyq9p35kv653a5f7z2cjkq37gvcqrd1"))))
    (properties `((upstream-name . "apeglm")))
    (build-system r-build-system)
    (propagated-inputs
@@ -6778,13 +8705,13 @@ posterior for individual coefficients.")
 (define-public r-greylistchip
   (package
    (name "r-greylistchip")
-   (version "1.28.1")
+   (version "1.30.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "GreyListChIP" version))
             (sha256
              (base32
-              "0w52vwvjarql19bsv40b80yn701qx8c9d0clsjhj85wmzj2p6dhg"))))
+              "02qzvs8fmh79g4cc5j2gxj1wazpmly7vjr527qlsgi3jmc3swxgz"))))
    (properties `((upstream-name . "GreyListChIP")))
    (build-system r-build-system)
    (propagated-inputs
@@ -6805,14 +8732,14 @@ signal in the input, that lead to spurious peaks during peak calling.")
 (define-public r-diffbind
   (package
     (name "r-diffbind")
-    (version "3.6.1")
+    (version "3.8.3")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DiffBind" version))
        (sha256
         (base32
-         "0izlk8vmmal4dj0bjxhgzr25arfa9zgdv06rm70w7ylr0gl84pzr"))))
+         "039gy9ll6ingh3y5h2hp3rhbh2imaryjxzgf8ysk87irlbpnx1qs"))))
     (properties `((upstream-name . "DiffBind")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6883,13 +8810,13 @@ processing to visualization and annotation.")
 (define-public r-mbkmeans
   (package
     (name "r-mbkmeans")
-    (version "1.12.0")
+    (version "1.14.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "mbkmeans" version))
               (sha256
                (base32
-                "1f5krzlyqljz763vkp1a50danjn78xhn35s8qqdvzrmwyx0fzphg"))))
+                "1ghv2j88p3sppqph3wxpm8z84nw7bi4idkn11wf806d8h1krfjm7"))))
     (build-system r-build-system)
     (native-inputs
      (list r-knitr))
@@ -6915,14 +8842,14 @@ large datasets, including support for on-disk data representation.")
 (define-public r-multtest
   (package
     (name "r-multtest")
-    (version "2.52.0")
+    (version "2.54.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "multtest" version))
        (sha256
         (base32
-         "037wcmwk1wvhjxgmlvnk289pkwishi1753ajkmy9x14xlmldix82"))))
+         "0ciz0fl0pzm4hjqw8af32s540lwjbkwvwnzgbfwadax40hgjs0g7"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-survival r-biocgenerics r-biobase r-mass))
@@ -6950,13 +8877,13 @@ expressed genes in DNA microarray experiments.")
 (define-public r-graph
   (package
     (name "r-graph")
-    (version "1.74.0")
+    (version "1.76.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "graph" version))
               (sha256
                (base32
-                "1b8hrjwjg82kicls1496fxfzv75xjvq2k6r9apzsd3qlbyg3ilg4"))))
+                "1hdbxjvgkxb9m341i9qbskb41g2z8qifkhgkpj2xb20s2dnxn3cc"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biocgenerics))
@@ -7013,6 +8940,35 @@ classification and ranking tasks.  @dfn{Area under curve} (AUC), precision at
 a given recall, F-score for single and multiple classes are available.")
     (license license:gpl2+)))
 
+(define-public r-pepsnmr
+  (package
+    (name "r-pepsnmr")
+    (version "1.16.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "PepsNMR" version))
+              (sha256
+               (base32
+                "02i29jinawssqlb33wvj0h9w6cfcvamlyfxdynd38jmwx23l15l5"))))
+    (properties `((upstream-name . "PepsNMR")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-ggplot2
+           r-gridextra
+           r-matrix
+           r-matrixstats
+           r-ptw
+           r-reshape2))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/ManonMartin/PepsNMR")
+    (synopsis "Pre-process 1H-NMR FID signals")
+    (description
+     "This package provides R functions for common pre-processing steps that
+are applied on @acronym{1H-NMR, proton nuclear magnetic resonance} data.  It
+also provides a function to read the @acronym{FID, free induction decay}
+signals directly in the Bruker format.")
+    (license license:gpl2)))
+
 ;; This is a CRAN package, but it depends on a Bioconductor package.
 (define-public r-codedepends
   (package
@@ -7043,14 +8999,14 @@ determining dependencies between variables, code improvement suggestions.")
 (define-public r-chippeakanno
   (package
     (name "r-chippeakanno")
-    (version "3.30.1")
+    (version "3.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChIPpeakAnno" version))
        (sha256
         (base32
-         "0a26glldxczcfymjvd45gv5m4hympziivm6wwx4ab9wld7n43l8y"))))
+         "13syh3mvqpaqgfndcrwdmn7815f4myxhzjga9a9q3lspci25rvy6"))))
     (properties `((upstream-name . "ChIPpeakAnno")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7097,13 +9053,13 @@ enrichedGO (addGeneIDs).")
 (define-public r-matrixgenerics
   (package
    (name "r-matrixgenerics")
-   (version "1.8.1")
+   (version "1.10.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "MatrixGenerics" version))
             (sha256
              (base32
-              "1liblnpziyyjxzrhdd5d89ilvfqqhbl87h3hsmdm0kwnmc73r37f"))))
+              "05a83gh5bvgadi2msgql5nmcgr8zp398rhdbmiqna608hqbymyq9"))))
    (properties
     `((upstream-name . "MatrixGenerics")))
    (build-system r-build-system)
@@ -7124,12 +9080,12 @@ incompatibilities.")
 (define-public r-marray
   (package
     (name "r-marray")
-    (version "1.74.0")
+    (version "1.76.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "marray" version))
               (sha256
-               (base32 "0awfz0akz3sylyw1jxhxgadv1rqdzvy9v11933yxkl9a8m9ngm8i"))))
+               (base32 "1bad4cjxv22h6vxxn86mxp7xvxhhzj81pikxq3h3hc2a858qfkgs"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-limma))
@@ -7143,12 +9099,12 @@ normalization and quality checking.")
 (define-public r-cghbase
   (package
    (name "r-cghbase")
-   (version "1.56.0")
+   (version "1.58.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "CGHbase" version))
             (sha256
-             (base32 "1q8yy60r4g5nyv2gbfdgk192xd73c0rrjr668d5616ddb7sx8wcr"))))
+             (base32 "01n1z525h4h6yr3jfalgjg2g6lhd77sc3n33q0485x7l6xqv1dvp"))))
    (properties `((upstream-name . "CGHbase")))
    (build-system r-build-system)
    (propagated-inputs
@@ -7162,12 +9118,12 @@ the @code{arrayCGH} packages.")
 (define-public r-cghcall
   (package
    (name "r-cghcall")
-   (version "2.58.0")
+   (version "2.60.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "CGHcall" version))
             (sha256
-             (base32 "1qpsibp4gb09sn6fkwwrdjkh3a28lqfbk18c6fvn4m386j96ps65"))))
+             (base32 "0860w2vf662qqii09pjdx85yl346jcldxiikhbwv0vg86blwb2g2"))))
    (properties `((upstream-name . "CGHcall")))
    (build-system r-build-system)
    (propagated-inputs
@@ -7181,12 +9137,12 @@ the @code{arrayCGH} packages.")
 (define-public r-qdnaseq
   (package
     (name "r-qdnaseq")
-    (version "1.32.0")
+    (version "1.34.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "QDNAseq" version))
               (sha256
-               (base32 "0s360s72lfn9vjml88gg1m40n61s0dc66ilzgfjdcp65djdxxfvm"))))
+               (base32 "1qv3vmc6i7r35pqhi45hmvg8h7v3bl82lv7yifs59k250zsdls59"))))
     (properties `((upstream-name . "QDNAseq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7213,14 +9169,14 @@ respectively.")
 (define-public r-bayseq
   (package
     (name "r-bayseq")
-    (version "2.30.0")
+    (version "2.31.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "baySeq" version))
        (sha256
         (base32
-         "1yqykndyv32s2rk7x86qf410qr0pigc8z4gdkl8vhj4dgyr47n2j"))))
+         "0lq2wfm3ibrpha9mqhhp6dgsx4jm2kwxvvrj0b62dzqspvg743wh"))))
     (properties `((upstream-name . "baySeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7237,14 +9193,14 @@ more complex hypotheses) via empirical Bayesian methods.")
 (define-public r-chipcomp
   (package
     (name "r-chipcomp")
-    (version "1.26.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChIPComp" version))
        (sha256
         (base32
-         "06q34y59gf1iz0rs7y5x8ndy1wa95j65rfmz37aym5c46ijqsnq0"))))
+         "1wnc7zrnnxk3nlk2l9y4il75dzirndp4vs5ivxn5rzqr6p7h4bhw"))))
     (properties `((upstream-name . "ChIPComp")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7271,14 +9227,14 @@ datasets.")
 (define-public r-riboprofiling
   (package
     (name "r-riboprofiling")
-    (version "1.26.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RiboProfiling" version))
        (sha256
         (base32
-         "08m4rc530bkzcc43iwzg2fw9cjlf4wc2d8akv5vblsb42xdn8sqp"))))
+         "0wmmpcabi1ngwmvfhxkp44kj1wvzyrcckkrzpjlzcq016lr67iwn"))))
     (properties `((upstream-name . "RiboProfiling")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7312,14 +9268,14 @@ assessment, principal component analysis on codon coverage.")
 (define-public r-riboseqr
   (package
     (name "r-riboseqr")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "riboSeqR" version))
        (sha256
         (base32
-         "1zs3y0icsqrndjp9wwqz3jxysvyc9pch45y49j6g9b5b2l44ma26"))))
+         "0la8kmxxh5jnqsrmmvyhi313bjdbqkiq16hcxar6mgyjhxlsm610"))))
     (properties `((upstream-name . "riboSeqR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7340,14 +9296,14 @@ parsing of genetic sequencing data from ribosome profiling experiments.")
 (define-public r-interactionset
   (package
     (name "r-interactionset")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "InteractionSet" version))
        (sha256
         (base32
-         "0qjimx25jvm8siq8hmlbf2z6mknzpbq945p06fsj826k57bpcsm5"))))
+         "14fb780f2g24ay28dy9xkmfziavbkj75v4vc2cmqbxfdsfp4yn0w"))))
     (properties
      `((upstream-name . "InteractionSet")))
     (build-system r-build-system)
@@ -7374,14 +9330,14 @@ experiments.")
 (define-public r-genomicinteractions
   (package
     (name "r-genomicinteractions")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GenomicInteractions" version))
        (sha256
         (base32
-         "0aph1hja5vfprxs3jl4zd1inhvih6m3v1p3jkm6w7xpj3jzvmgbx"))))
+         "0l14hz5pr0wlin46y8ycpvk5hp2ld9ajx11y85rw5hlwv50byfbb"))))
     (properties
      `((upstream-name . "GenomicInteractions")))
     (build-system r-build-system)
@@ -7415,14 +9371,14 @@ information and producing various plots and statistics.")
 (define-public r-ctc
   (package
     (name "r-ctc")
-    (version "1.70.0")
+    (version "1.72.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ctc" version))
        (sha256
         (base32
-         "0c9pgp25dqx12fmi4cqm7xyxjmy6g7wv9vbljgdjghaij2lrc4pb"))))
+         "098a65fk9la639sqihhsghhgb3hyzv35j6akph908zwq5grsv0c5"))))
     (build-system r-build-system)
     (propagated-inputs (list r-amap))
     (home-page "https://bioconductor.org/packages/ctc/")
@@ -7435,14 +9391,14 @@ trees and clusters to other programs.")
 (define-public r-goseq
   (package
     (name "r-goseq")
-    (version "1.48.0")
+    (version "1.50.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "goseq" version))
        (sha256
         (base32
-         "1w0rwzhqkvp2x7y5v0qcyjbss0p95gb1jrnx5sdkqginbvrmrd48"))))
+         "0x89lv84l3qcahca54njcza326553zij2xyagy18mwlprdrq4iy8"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotationdbi
@@ -7461,14 +9417,14 @@ defined categories which are over/under represented in RNA-seq data.")
 (define-public r-glimma
   (package
     (name "r-glimma")
-    (version "2.6.0")
+    (version "2.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Glimma" version))
        (sha256
         (base32
-         "1k17ay09vhb2hakg1vrgvpp1zliavlj7cdkxaal162bc3v8pyvyz"))))
+         "1fskabpd3xlrbhqvzam9ibpxmbdys7y1b265np8hz4k704ww1g22"))))
     (properties `((upstream-name . "Glimma")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7491,17 +9447,52 @@ representations of analysis results in order to provide additional
 information.")
     (license license:lgpl3)))
 
+(define-public r-glmgampoi
+  (package
+    (name "r-glmgampoi")
+    (version "1.10.1")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "glmGamPoi" version))
+              (sha256
+               (base32
+                "1qxzbh5i208cpghmysailachj8xpx4g4iqk8552xjpjkn54pkpbd"))))
+    (properties `((upstream-name . "glmGamPoi")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-beachmat
+           r-biocgenerics
+           r-delayedarray
+           r-delayedmatrixstats
+           r-hdf5array
+           r-matrixgenerics
+           r-matrixstats
+           r-rcpp
+           r-rcpparmadillo
+           r-rlang
+           r-singlecellexperiment
+           r-summarizedexperiment))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/const-ae/glmGamPoi")
+    (synopsis "Fit a Gamma-Poisson Generalized Linear Model")
+    (description
+     "Fit linear models to overdispersed count data.  The package can estimate
+the overdispersion and fit repeated models for matrix input.  It is designed
+to handle large input datasets as they typically occur in single cell RNA-seq
+experiments.")
+    (license license:gpl3)))
+
 (define-public r-rots
   (package
     (name "r-rots")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ROTS" version))
        (sha256
         (base32
-         "021a578p8kcl5yd9myiy0h2qp10r30ggnip2kp6xs7dx8nzic96r"))))
+         "1wirblji4ckiwrvnh14cfwc9cjypazbaqr00ka5ndyz39cc31shn"))))
     (properties `((upstream-name . "ROTS")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7517,14 +9508,14 @@ in omics data.")
 (define-public r-plgem
   (package
     (name "r-plgem")
-    (version "1.68.0")
+    (version "1.70.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "plgem" version))
        (sha256
         (base32
-         "07zxflxcay17hxjw3wh5kfdwl2x8537csb18p1qzmyrkvscnja77"))))
+         "0hnhfdrlg4907dc4s17cy4kgmq5nr616f1wi7jn72acxwqfl4bk8"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase r-mass))
@@ -7541,14 +9532,14 @@ genes or proteins in these datasets.")
 (define-public r-inspect
   (package
     (name "r-inspect")
-    (version "1.26.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "INSPEcT" version))
        (sha256
         (base32
-         "0jx887vhxwd8zlqajr9czvn9nx88ryyxlnl58hxrlajjpcjkz9ax"))))
+         "126cbanan2fr916spacw6lm8hzkys56k7z3gq0r351zd7q13gky3"))))
     (properties `((upstream-name . "INSPEcT")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7587,14 +9578,14 @@ modeling the rates that determines changes in mature mRNA levels.")
 (define-public r-dnabarcodes
   (package
     (name "r-dnabarcodes")
-    (version "1.26.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DNABarcodes" version))
        (sha256
         (base32
-         "0n2qlvpcjhrxr3br27gz9vhwcpf7sn6g4xdjazvvi3gqcgk90xc6"))))
+         "18sivwzl8gk52dnhwls0i4imw78rkjlwbfrcaas1i53q0bmw15i5"))))
     (properties `((upstream-name . "DNABarcodes")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7614,14 +9605,14 @@ demultiplexed, i.e. assigned to their original reference barcode.")
 (define-public r-ruvseq
   (package
     (name "r-ruvseq")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RUVSeq" version))
        (sha256
         (base32
-         "001h07b074hvj16bjdp9llb9psphw7r6kpwhq61bj4519y6lpg7x"))))
+         "1qb4k7pm8w86d2p9q2r4n63iyi34wdib5x9rsjx4vhcxrnzyyygm"))))
     (properties `((upstream-name . "RUVSeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7639,14 +9630,14 @@ samples.")
 (define-public r-biocneighbors
   (package
     (name "r-biocneighbors")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocNeighbors" version))
        (sha256
         (base32
-         "1a43hzmcpxviqa9723hkafr6gm358amfpqj9d56imclkkfkdz95x"))))
+         "09f00rf5gwwlxxaycsciq4l53gjg5kjayx8xzhns2yf1fv297j9p"))))
     (properties `((upstream-name . "BiocNeighbors")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7667,14 +9658,14 @@ achieved for all methods using the BiocParallel framework.")
 (define-public r-scaledmatrix
   (package
     (name "r-scaledmatrix")
-    (version "1.4.0")
+    (version "1.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ScaledMatrix" version))
        (sha256
         (base32
-         "0p6065mbn77hphpjfchz3r3raspl127f11n39mwh9bih4zg375cl"))))
+         "0lxr6z9zdrgvm06inc1d8gl2agqmbjvgs8f5ryn5x68hqlnchnl1"))))
     (properties `((upstream-name . "ScaledMatrix")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7693,14 +9684,14 @@ multiplication.")
 (define-public r-treeio
   (package
     (name "r-treeio")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "treeio" version))
        (sha256
         (base32
-         "1hc5m0b2qqxrh3z0inny2jizrpn9d4yn9pn3k1h18xb4ggyijyla"))))
+         "1xl8497ya79hlp3v3fihnz9grwni29v6860i273lrpcljv8868l9"))))
     (properties `((upstream-name . "treeio")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7722,22 +9713,56 @@ heterogeneous associated data to a single tree file and can be served as a
 platform for merging tree with associated data and converting file formats.")
     (license license:artistic2.0)))
 
+(define-public r-treesummarizedexperiment
+  (package
+    (name "r-treesummarizedexperiment")
+    (version "2.6.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "TreeSummarizedExperiment" version))
+              (sha256
+               (base32
+                "136zgpn1l059i64gj6iappr6nz42z4wbxlg3zpc5npwkqrz3val2"))))
+    (properties `((upstream-name . "TreeSummarizedExperiment")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-ape
+           r-biocgenerics
+           r-biocparallel
+           r-biostrings
+           r-dplyr
+           r-iranges
+           r-rlang
+           r-s4vectors
+           r-singlecellexperiment
+           r-summarizedexperiment
+           r-treeio))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/TreeSummarizedExperiment")
+    (synopsis "S4 class for data with tree structures")
+    (description
+     "@code{TreeSummarizedExperiment} extends @code{SingleCellExperiment} to
+include hierarchical information on the rows or columns of the rectangular
+data.")
+    (license license:gpl2+)))
+
 (define-public r-ggtree
   (package
     (name "r-ggtree")
-    (version "3.4.0")
+    (version "3.6.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ggtree" version))
        (sha256
         (base32
-         "033r748npv0l72yb9sk6lqnj0l7cd36ykf788145qv8ck5i2gyk4"))))
+         "177nq6arhxp0x6zsf2c6cn3xxwfk65dihbpni6mb9ifgnmfqdjmx"))))
     (properties `((upstream-name . "ggtree")))
     (build-system r-build-system)
     (propagated-inputs
      (list r-ape
            r-aplot
+           r-cli
            r-dplyr
            r-ggfun
            r-ggplot2
@@ -7762,14 +9787,14 @@ data.")
 (define-public r-metapod
   (package
     (name "r-metapod")
-    (version "1.4.0")
+    (version "1.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "metapod" version))
        (sha256
         (base32
-         "19g9c08alg4qqr710si465wlb5dy759m5d8wn91zwj24077dds7b"))))
+         "06ala1qz9bfq7nnj92m0c5r85kk7h4zrljjh0hgrap5sjlsm09bb"))))
     (properties `((upstream-name . "metapod")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7791,14 +9816,14 @@ missing values and weighting where appropriate.")
 (define-public r-biocsingular
   (package
     (name "r-biocsingular")
-    (version "1.12.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocSingular" version))
        (sha256
         (base32
-         "1sraycnn0jahpi8kni1y8ik00ga89fvwqjmbr8388968q22mvm3x"))))
+         "041izymcifvi0pa97fh5000bwlyl0mdk9003i5bbvlld6mbbv2kk"))))
     (properties `((upstream-name . "BiocSingular")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7826,14 +9851,14 @@ possible, parallelization is achieved using the BiocParallel framework.")
 (define-public r-destiny
   (package
     (name "r-destiny")
-    (version "3.10.0")
+    (version "3.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "destiny" version))
        (sha256
         (base32
-         "1c85ky5ggdsi0ab1l4ipl85gc1kj1zv3wp08qrvslax3z0yw0ljy"))))
+         "0rgd723azjrdxv441k96vircqb18w31q0ljhksbdrvcp9qb85r6i"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase
@@ -7870,14 +9895,14 @@ maps.")
 (define-public r-savr
   (package
     (name "r-savr")
-    (version "1.34.0")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "savR" version))
        (sha256
         (base32
-         "04zlf3lyr6vnpj80m6fd2is2f7302sxwih8nzzjnc4ss972jid2k"))))
+         "1b7kjgj2r6lgkdnrq91wcwvwb5an0gfdsbyp7j0pvn2byfm4lply"))))
     (properties `((upstream-name . "savR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7892,14 +9917,14 @@ Viewer (SAV) files, access data, and generate QC plots.")
 (define-public r-chipexoqual
   (package
     (name "r-chipexoqual")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChIPexoQual" version))
        (sha256
         (base32
-         "1r4s8awvwwj1g33jpnzfxji23mfy0chkhi14i0ml5sh090xijpaz"))))
+         "0k4vbdwpp7z06fzjgqnmrx2yllayc0z2baj26bh4vji5vb48k9ik"))))
     (properties `((upstream-name . "ChIPexoQual")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7932,13 +9957,13 @@ sequencing data.")
 (define-public r-copynumber
   (package
     (name "r-copynumber")
-    (version "1.36.0")
+    (version "1.38.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "copynumber" version))
               (sha256
                (base32
-                "1gr8q9ri49x8qlmbsi6k6wcak1w9v48wr1qy7axc86brzx6z6mhd"))))
+                "1a664bllaq9pbb5cpd01j919qirylvnm8qd49lwlz89jvqjdri19"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-s4vectors r-iranges r-genomicranges r-biocgenerics))
@@ -7952,14 +9977,14 @@ penalized least squares regression method.")
 (define-public r-dnacopy
   (package
     (name "r-dnacopy")
-    (version "1.70.0")
+    (version "1.72.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DNAcopy" version))
        (sha256
         (base32
-         "10bh4p8nbl84rfngsm3bi9w542m159kff95f8c2hvjcxv5yw7iwc"))))
+         "1f6ilfwhli7bdnr48y2ijdydvw7kjbyz701kgbsw3w7inr6x6ayr"))))
     (properties `((upstream-name . "DNAcopy")))
     (build-system r-build-system)
     (native-inputs (list gfortran))
@@ -8050,14 +10075,14 @@ and regression inferences from RNA-sequencing data.")
 (define-public r-ebseq
   (package
     (name "r-ebseq")
-    (version "1.36.0")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "EBSeq" version))
        (sha256
         (base32
-         "192xl9fwsh04w563yk33mfl303d1kqby2ssbqkckqsdr4jb7d57y"))))
+         "1gh1cyb76gv2h0knh780648gsbgpn76adfj6x3pjzily5m5bmin0"))))
     (properties `((upstream-name . "EBSeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8072,13 +10097,13 @@ gene and isoform level using RNA-seq data")
 (define-public r-karyoploter
   (package
     (name "r-karyoploter")
-    (version "1.22.0")
+    (version "1.24.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "karyoploteR" version))
               (sha256
                (base32
-                "0hawq9wi3ikvlcdgnjfy5fiiwfq22zwx1p8xf5h4bpypp96pknsk"))))
+                "1dcxq3651903wwzr7bww8c4wd8h5h7rklnqfgklqpss0psx59d2w"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotationdbi
@@ -8110,14 +10135,14 @@ coordinates.")
 (define-public r-lpsymphony
   (package
     (name "r-lpsymphony")
-    (version "1.24.0")
+    (version "1.26.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "lpsymphony" version))
        (sha256
         (base32
-         "0kc708ss5byzw8qh439mb4nq6hsfmz73gfamiznw3lv352brd33g"))))
+         "167zpf7k7gn7gw2cxkqx89y322qinyzjr1naracp5axj4q2qagm3"))))
     (build-system r-build-system)
     (arguments
      (list
@@ -8149,14 +10174,14 @@ to install interface to SYMPHONY.")
 (define-public r-ihw
   (package
     (name "r-ihw")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "IHW" version))
        (sha256
         (base32
-         "1gsfy75dz7xh16z844llcmjnp0a0ridszmrbbv2bdaa43na5msmf"))))
+         "04vbf42bzqydf5mi4mqmcyh0xdx4phs4cjhsm6fimhmjhxm8jyry"))))
     (properties `((upstream-name . "IHW")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8178,14 +10203,14 @@ independent of the p-value under the null hypothesis.")
 (define-public r-icobra
   (package
     (name "r-icobra")
-    (version "1.24.1")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "iCOBRA" version))
        (sha256
         (base32
-         "1gvra5bgsf6lvs4f2md3xx7xxsx4j8079c2nr8vz9lvy2sfyl6s9"))))
+         "0mh7arn5rv26picz05ywil5ynras91xv6diwh47s9ip75vp9s3cy"))))
     (properties `((upstream-name . "iCOBRA")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8215,14 +10240,14 @@ interactive exploration of results.")
 (define-public r-residualmatrix
   (package
     (name "r-residualmatrix")
-    (version "1.6.0")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ResidualMatrix" version))
        (sha256
         (base32
-         "1pjr3gva0jwj2pgqr4k4nl1ir1153hhrk1d400r30w0di472hns4"))))
+         "0zqifr1zhsfhrkjlp0ajqiqc9f96yz8zr13yhl19lvw30pwg9rj9"))))
     (properties
      `((upstream-name . "ResidualMatrix")))
     (build-system r-build-system)
@@ -8244,14 +10269,14 @@ multiplication and calculation of row/column sums or means.")
 (define-public r-batchelor
   (package
     (name "r-batchelor")
-    (version "1.12.3")
+    (version "1.14.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "batchelor" version))
        (sha256
         (base32
-         "00ix3hvhgalxg63qnynv2waa273jk336lg47k72qwxfzimsxfjxc"))))
+         "1yj84ba6px14hbqg8526527vfcxmzvmly34f7hba4vybdm1jscfm"))))
     (properties `((upstream-name . "batchelor")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8287,14 +10312,14 @@ the numbers of cells across batches.")
 (define-public r-mast
   (package
     (name "r-mast")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MAST" version))
        (sha256
         (base32
-         "1kmrqxcfzzcs8l33n9qn0vahc6wxq6ks3cjx95vg96maf2qzhzzi"))))
+         "133ijkw5sd0gl38dfr7qfqvvp2df7lg6j8vkvy54zlpamkg6l2x1"))))
     (properties `((upstream-name . "MAST")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8322,14 +10347,14 @@ single cell assay data.")
 (define-public r-monocle
   (package
     (name "r-monocle")
-    (version "2.24.1")
+    (version "2.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "monocle" version))
        (sha256
         (base32
-         "11g1wx0f1yzhg3x1aa3d5l7pqlzxj16s0gha21skxkgld8k2x8xn"))))
+         "1d3xgh9xgqa28bgyd06zkjmg75lq7hdah3d140l1bqq2ii1bv62g"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase
@@ -8507,14 +10532,14 @@ user-defined and/or data-driven sets of hypotheses.")
 (define-public r-noiseq
   (package
     (name "r-noiseq")
-    (version "2.40.0")
+    (version "2.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "NOISeq" version))
        (sha256
         (base32
-         "0ah6adlhv4254jkssinn2ik8n811hd1nw85bnzqk2kwhl49nrk27"))))
+         "1j0yafl5r1vsn99zkhvaz2mrwv37l4p8ldgiq09d9hxpjq9ls7i2"))))
     (properties `((upstream-name . "NOISeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8533,14 +10558,14 @@ assumptions.")
 (define-public r-scdd
   (package
     (name "r-scdd")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scDD" version))
        (sha256
         (base32
-         "0bjww338z5qf2g97kbh85h9kpagjr59ff9f4alm33h16xz5mb7k0"))))
+         "0kmnmlzww2xfd04lp9nsh0wkigab9ipgqlsn2jrd77fizpd0kvwg"))))
     (properties `((upstream-name . "scDD")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8571,14 +10596,14 @@ distributions.")
 (define-public r-scone
   (package
     (name "r-scone")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scone" version))
        (sha256
         (base32
-         "05id34n6min03ha1chg5mrvx399qm2mby9kxkaz5w8fbidp97851"))))
+         "0pg09r28xqjlvb6nbswglnmwi05q63fag6rp3sw41g6z8gm5wap7"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-aroma-light
@@ -8615,14 +10640,14 @@ high-throughput analyses.")
 (define-public r-geoquery
   (package
     (name "r-geoquery")
-    (version "2.64.2")
+    (version "2.66.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GEOquery" version))
        (sha256
         (base32
-         "1cvkvq2haz831qi8w0gd3ayvxfxsl0z5klhki4gkfi9xqdv1gi9x"))))
+         "0ck2aml1kxdahwcszi3j7hcikwi8fdnzphlrsn3h2q4dkk5x00kn"))))
     (properties `((upstream-name . "GEOquery")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8650,14 +10675,14 @@ the bridge between GEO and BioConductor.")
 (define-public r-illuminaio
   (package
     (name "r-illuminaio")
-    (version "0.38.0")
+    (version "0.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "illuminaio" version))
        (sha256
         (base32
-         "1xk057a9w4ps8xi8jyw8imkjcicfmzns8g92grn4af7yiip68h62"))))
+         "1cw526mbhh0czkwk99qnr6hfwi4k4xi2bm5p14kw9sr00if59x12"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-base64))
@@ -8671,14 +10696,14 @@ files, including IDAT.")
 (define-public r-siggenes
   (package
     (name "r-siggenes")
-    (version "1.70.0")
+    (version "1.72.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "siggenes" version))
        (sha256
         (base32
-         "0amjqm2c8p1vjzx109p7n81wbsbx8rljwn6mbkl7dpi834im9d7l"))))
+         "0gis34s56y4xa61a9gywjwgd6525ywasa6r4xxhj3rshh1dz5jkv"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase r-multtest r-scrime))
@@ -8695,14 +10720,14 @@ Bayes Analyses of Microarrays} (EBAM).")
 (define-public r-bumphunter
   (package
     (name "r-bumphunter")
-    (version "1.38.0")
+    (version "1.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bumphunter" version))
        (sha256
         (base32
-         "0k92ps9chqsimbc7vsr8swg679zfv8nfn5zahbqq4nknhhy7hwxw"))))
+         "0jwbhd2fhm1w5slwhz8krnw835a8qb4akm3n3pv867bvi0xnp3g2"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotationdbi
@@ -8726,16 +10751,101 @@ to identify differentially methylated regions in epigenetic epidemiology
 studies.")
     (license license:artistic2.0)))
 
+(define-public r-mia
+  (package
+    (name "r-mia")
+    (version "1.6.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "mia" version))
+              (sha256
+               (base32
+                "0yz88ggv6d5rccdwzixwg9y1bc4xysazlmv1ph88wxs8r6fcmync"))))
+    (properties `((upstream-name . "mia")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-ape
+           r-biocgenerics
+           r-biocparallel
+           r-biostrings
+           r-decipher
+           r-decontam
+           r-delayedarray
+           r-delayedmatrixstats
+           r-dirichletmultinomial
+           r-dplyr
+           r-iranges
+           r-mass
+           r-multiassayexperiment
+           r-rlang
+           r-s4vectors
+           r-scater
+           r-scuttle
+           r-singlecellexperiment
+           r-summarizedexperiment
+           r-tibble
+           r-tidyr
+           r-treesummarizedexperiment
+           r-vegan))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/microbiome/mia")
+    (synopsis "Microbiome analysis")
+    (description
+     "The mia package implements tools for microbiome analysis based on the
+@code{SummarizedExperiment}, @code{SingleCellExperiment} and
+@code{TreeSummarizedExperiment} infrastructure.  Data wrangling and analysis
+in the context of taxonomic data is the main scope.  Additional functions for
+common task are implemented such as community indices calculation and
+summarization.")
+    (license license:artistic2.0)))
+
+(define-public r-microbiome
+  (package
+    (name "r-microbiome")
+    (version "1.20.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "microbiome" version))
+              (sha256
+               (base32
+                "1j3lrrz6yxfzsr037c0bbdhrs0ll7jg0mpcvk3iqdryi5rysnx0x"))))
+    (properties `((upstream-name . "microbiome")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biostrings
+           r-compositions
+           r-dplyr
+           r-ggplot2
+           r-phyloseq
+           r-reshape2
+           r-rtsne
+           r-scales
+           r-tibble
+           r-tidyr
+           r-vegan))
+    (native-inputs (list r-knitr))
+    (home-page "https://microbiome.github.io/microbiome/")
+    (synopsis "Tools for microbiome analysis")
+    (description
+     "This package facilitates phyloseq exploration and analysis of taxonomic
+profiling data.  This package provides tools for the manipulation, statistical
+analysis, and visualization of taxonomic profiling data.  In addition to
+targeted case-control studies, microbiome facilitates scalable exploration of
+population cohorts.  This package supports the independent phyloseq data
+format and expands the available toolkit in order to facilitate the
+standardization of the analyses and the development of best practices.")
+    (license license:bsd-2)))
+
 (define-public r-milor
   (package
     (name "r-milor")
-    (version "1.4.0")
+    (version "1.6.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "miloR" version))
               (sha256
                (base32
-                "1jz9p3grnczx0bpdw6j64x21in8zgm3qy19hmm296har2rx9m5zs"))))
+                "07p9rs1jmgxqaahjbrnvvs94c142n2qfw8ip3qqkr6mhzwr19ly3"))))
     (properties `((upstream-name . "miloR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8777,14 +10887,14 @@ model.")
 (define-public r-minfi
   (package
     (name "r-minfi")
-    (version "1.42.0")
+    (version "1.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "minfi" version))
        (sha256
         (base32
-         "0255z7w5i5k01w8wn7jkb37h3q7m7vg0szqgk76h330yydnmkrq6"))))
+         "15989zilgy2j4k4nw046qg8wli7ynjh2b1yzfv7cwgn87mp618lc"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-beanplot
@@ -8828,14 +10938,14 @@ methylation arrays.")
 (define-public r-methylumi
   (package
     (name "r-methylumi")
-    (version "2.42.0")
+    (version "2.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "methylumi" version))
        (sha256
         (base32
-         "0klkinq55lfj1d4z8gkrv98849079x1l5gd15habw7jq9xxvhjww"))))
+         "07kfyv3kkayzh0akxfl3p9gckw8qiplkxbyxw8npc7cb03ihgmc4"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotate
@@ -8875,14 +10985,14 @@ and Infinium HD arrays are also included.")
 (define-public r-lumi
   (package
     (name "r-lumi")
-    (version "2.48.0")
+    (version "2.50.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "lumi" version))
        (sha256
         (base32
-         "06zmll5j1yymsm3byarhllrz4q1w5mzv267a9g6visn73wan8y9d"))))
+         "1091458is69dxnjrcd11czqy55c68sdnkrmpvlm6hw2cbghs2bjq"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-affy
@@ -8914,14 +11024,14 @@ especially Illumina Infinium methylation microarrays.")
 (define-public r-linnorm
   (package
     (name "r-linnorm")
-    (version "2.20.0")
+    (version "2.22.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Linnorm" version))
        (sha256
         (base32
-         "1002lllgns5klv3q2wsikkbypa2bafpka7a8mri0y5bfxncfr2zb"))))
+         "16d7viyidqbsy3mbr2cpq9p291yf362a4blhvs05qxcwm3fjllij"))))
     (properties `((upstream-name . "Linnorm")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8975,14 +11085,14 @@ evaluation of DEG analysis methods.")
 (define-public r-ioniser
   (package
     (name "r-ioniser")
-    (version "2.20.0")
+    (version "2.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "IONiseR" version))
        (sha256
         (base32
-         "0cgx1dcfh617l9vr4r3ky8w7f0snl0vpavfd9n1h5n68p0p42dwi"))))
+         "1xkxqavhcw22lhij87cpd5ps1ldkzzi0pp93d38pxbbhj15gc3d3"))))
     (properties `((upstream-name . "IONiseR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9071,13 +11181,13 @@ published results; and a routine for graphical display.")
 (define-public r-tradeseq
   (package
    (name "r-tradeseq")
-   (version "1.10.0")
+   (version "1.12.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "tradeSeq" version))
             (sha256
              (base32
-              "0v9nqxrwa69qhmyaicn2vvs8haha4kzs93iqim306331vadp9qm0"))))
+              "0wkbjhwqk094nd5h6sl2nw5jp5vmkh9why635l8qkqmxa2jm3gh0"))))
    (build-system r-build-system)
    (propagated-inputs
     (list r-biobase
@@ -9140,14 +11250,14 @@ peak definition in combination with known profile characteristics.")
 (define-public r-varianttools
   (package
     (name "r-varianttools")
-    (version "1.38.0")
+    (version "1.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "VariantTools" version))
        (sha256
         (base32
-         "18nxcamfgnw4n2ab0czxglw0sqc9wzdqzpjv43lcyyal23lzzsix"))))
+         "181igcmlyx3ddmhml9wqcgw6ffdrqpmg4imd6ipf68c90agdgaz0"))))
     (properties `((upstream-name . "VariantTools")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9180,14 +11290,14 @@ gmapR.")
 (define-public r-heatplus
   (package
     (name "r-heatplus")
-    (version "3.4.0")
+    (version "3.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Heatplus" version))
        (sha256
         (base32
-         "0b1mzxysmrqinp93p587apna8p0llmawblwj93icydqxxm2jkhb1"))))
+         "0zbjw9f616dz1fpp6q6whbmlrf2gypq8pp9i66c376cs2aifp1si"))))
     (properties `((upstream-name . "Heatplus")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9205,14 +11315,14 @@ information about samples and features can be added to the plot.")
 (define-public r-gosemsim
   (package
     (name "r-gosemsim")
-    (version "2.22.0")
+    (version "2.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GOSemSim" version))
        (sha256
         (base32
-         "1hp15pzd0m0g9f8kglyfsgjqxnvxcmm9022xnsrkzfvmj2yw14vd"))))
+         "14wc7qgk1psknld05246cn0nqxpbjprax7j75h5yyd0w7hjyly2s"))))
     (properties `((upstream-name . "GOSemSim")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9232,14 +11342,14 @@ sets of GO terms, gene products and gene clusters.")
 (define-public r-anota
   (package
     (name "r-anota")
-    (version "1.44.0")
+    (version "1.46.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "anota" version))
        (sha256
         (base32
-         "1x75r5znl8jllqsgzpxsqj62ch11bpwhmyzmbjmb8sz8f8ww923c"))))
+         "1a9xgcp48zjql6an3kiv8li4saw10k1dl7qzyyw84xvx856ilv97"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-multtest r-qvalue))
@@ -9262,14 +11372,14 @@ the data set is suitable for such analysis.")
 (define-public r-sigpathway
   (package
     (name "r-sigpathway")
-    (version "1.64.0")
+    (version "1.66.1")
     (source
       (origin
         (method url-fetch)
         (uri (bioconductor-uri "sigPathway" version))
         (sha256
           (base32
-            "1c2kwhbxgf66az7ssm2mab9n5x59zy4kxq8vblz5r9636xqaysif"))))
+            "1ln1n4zwmjw1ils45vix93q3h19xlg4q894yhhxkphgyj0qcy00b"))))
     (properties `((upstream-name . "sigPathway")))
     (build-system r-build-system)
     (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
@@ -9284,13 +11394,13 @@ phenotype of interest.")
 (define-public r-fcscan
   (package
     (name "r-fcscan")
-    (version "1.10.0")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "fcScan" version))
        (sha256
-        (base32 "0yv7ifw0xxx1v9z8dxszv0cb72q3frd74dyxfbvrcs6x9y9v3jzp"))))
+        (base32 "0z83ncjxw9x8nvc6pncrvpf6lmamvgrv56j96s1f0x9jydk18chy"))))
     (properties `((upstream-name . "fcScan")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9317,22 +11427,22 @@ presence of additional sites within the allowed window size.")
 (define-public r-fgsea
   (package
     (name "r-fgsea")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "fgsea" version))
        (sha256
         (base32
-         "0innyggai6l4fpl4qrblzdc52vqw9jaszmip0yr1lv7rzwyl6mpg"))))
+         "1frl5mchbrgqyxxdlw76qqq5i8vv2fdmy8xl8h8c8cvvmlz393qk"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-bh
            r-biocparallel
+           r-cowplot
            r-data-table
            r-fastmatch
            r-ggplot2
-           r-gridextra
            r-matrix
            r-rcpp))
     (native-inputs
@@ -9349,23 +11459,23 @@ to multiple hypothesis correction.")
 (define-public r-dose
   (package
     (name "r-dose")
-    (version "3.22.0")
+    (version "3.24.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DOSE" version))
        (sha256
         (base32
-         "11lg4ql0bi54p2wg3z1dw9rwqai37khgcqbs4cb7zf67ml8jadwp"))))
+         "0scp6sgb1iwwfh7gdak4dxf1hb870745km9nc9hga8pnsnqi5v3g"))))
     (properties `((upstream-name . "DOSE")))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotationdbi
            r-biocparallel
-           r-do-db
            r-fgsea
            r-ggplot2
            r-gosemsim
+           r-hdo-db
            r-qvalue
            r-reshape2))
     (native-inputs
@@ -9384,20 +11494,21 @@ data.")
 (define-public r-enrichplot
   (package
     (name "r-enrichplot")
-    (version "1.16.1")
+    (version "1.18.3")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "enrichplot" version))
        (sha256
         (base32
-         "17ln1wbkq8sp7jw0dpkccj5qcsl382sgd7zic04dk99z9ag3mh02"))))
+         "0nzcr23m58z3h0n0frxf26z14j7ilcl4fjy7rqm7f2i1wyld70zl"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-aplot
            r-dose
            r-ggplot2
            r-ggraph
+           r-ggnewscale
            r-ggtree
            r-gosemsim
            r-igraph
@@ -9406,6 +11517,7 @@ data.")
            r-purrr
            r-rcolorbrewer
            r-reshape2
+           r-rlang
            r-scatterpie
            r-shadowtext
            r-yulab-utils))
@@ -9422,14 +11534,14 @@ All the visualization methods are developed based on ggplot2 graphics.")
 (define-public r-clusterprofiler
   (package
     (name "r-clusterprofiler")
-    (version "4.4.4")
+    (version "4.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "clusterProfiler" version))
        (sha256
         (base32
-         "0k5jhry0j6wa7779n3hrw4ld4bvyahpgpbwi2a0g704m3dd3mqp5"))))
+         "0fm2cz2464xh075p4yl6bha9m6didc41ng4a3flkw1f1cvvpi4g0"))))
     (properties
      `((upstream-name . "clusterProfiler")))
     (build-system r-build-system)
@@ -9441,6 +11553,7 @@ All the visualization methods are developed based on ggplot2 graphics.")
            r-enrichplot
            r-go-db
            r-gosemsim
+           r-gson
            r-magrittr
            r-plyr
            r-qvalue
@@ -9459,13 +11572,13 @@ profiles (GO and KEGG) of gene and gene clusters.")
 (define-public r-clusterexperiment
   (package
     (name "r-clusterexperiment")
-    (version "2.16.0")
+    (version "2.18.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "clusterExperiment" version))
               (sha256
                (base32
-                "1xd2kxmdg51hhj0zvz7pxmpdvb1sya7prsf9ny2wj2y8ivrqgn4f"))))
+                "1f3f56d88yiqyj45rhcwqb04wbxr9m4fxhbbckw1j7nykm8100ps"))))
     (build-system r-build-system)
     (native-inputs
      (list r-knitr))
@@ -9505,14 +11618,14 @@ expression data sets.")
 (define-public r-mlinterfaces
   (package
     (name "r-mlinterfaces")
-    (version "1.76.0")
+    (version "1.78.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MLInterfaces" version))
        (sha256
         (base32
-         "179d19kxjipfkc40z15337x1vzqd7vz3gbmr2lw5w7x9l857ngs5"))))
+         "0xnaghm65ydk01gzx5g38jyq7vfdw206c2w59k0qg8lhy9fqky9x"))))
     (properties `((upstream-name . "MLInterfaces")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9535,6 +11648,7 @@ expression data sets.")
            r-rpart
            r-sfsmisc
            r-shiny
+           r-summarizedexperiment
            r-threejs))
     (home-page "https://bioconductor.org/packages/MLInterfaces/")
     (synopsis "Interfaces to R machine learning procedures")
@@ -9547,14 +11661,14 @@ data in R and Bioconductor containers.")
 (define-public r-annaffy
   (package
     (name "r-annaffy")
-    (version "1.68.0")
+    (version "1.70.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "annaffy" version))
        (sha256
         (base32
-         "1fbqknwbl4534h66xrhcryg9pavm9fkja47gqbsxf8bd5yhk5mgq"))))
+         "0qxihlhx7ijspvgzdp8zxzrc44y9pwkygvsllh4v47p85ham49fg"))))
     (build-system r-build-system)
     (arguments
      `(#:phases
@@ -9579,14 +11693,14 @@ It allows searching of biological metadata using various criteria.")
 (define-public r-a4core
   (package
     (name "r-a4core")
-    (version "1.44.0")
+    (version "1.46.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "a4Core" version))
        (sha256
         (base32
-         "1ky1lphq6bqxj6h12pg06cvs451fziqam8gd56wmpk6r5pbg4390"))))
+         "0plgfzsvg220v6k6p0g7izsfw2lj78331lqyvz0p9vd91ynwp41k"))))
     (properties `((upstream-name . "a4Core")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9603,14 +11717,14 @@ arrays.")
 (define-public r-a4classif
   (package
     (name "r-a4classif")
-    (version "1.44.0")
+    (version "1.46.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "a4Classif" version))
        (sha256
         (base32
-         "1v61vgpqrf7bhk44n2gkxb8dm5d0rr8c9rd6fdcjs50nhij0lbiw"))))
+         "0lirj0qzzrm996g8yh30x61cg1qkh436qd8xzgv3y3y3n5jj5d3w"))))
     (properties `((upstream-name . "a4Classif")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9633,14 +11747,14 @@ Affymetrix arrays.")
 (define-public r-a4preproc
   (package
     (name "r-a4preproc")
-    (version "1.44.0")
+    (version "1.46.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "a4Preproc" version))
        (sha256
         (base32
-         "098yzy7x5536bj76iavismdsdn7x6x07aw0j3knj6i9www9y8yz9"))))
+         "00xs1vayl8v6in79iv7lwbn52yyyq4lv6k3k727g7il8x17mi8i0"))))
     (properties `((upstream-name . "a4Preproc")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9657,14 +11771,14 @@ is used for preprocessing the arrays.")
 (define-public r-a4reporting
   (package
     (name "r-a4reporting")
-    (version "1.44.0")
+    (version "1.46.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "a4Reporting" version))
        (sha256
         (base32
-         "03sypayh187gqc6hykkqr1g0vb3zxc2c3xyp00jfbn12b35acnb0"))))
+         "09q8ng5kp47bqpj7m2y2112fkjxcnhzxk9v80hqksm8h1df46riv"))))
     (properties `((upstream-name . "a4Reporting")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9681,14 +11795,14 @@ provides reporting features.")
 (define-public r-a4base
   (package
     (name "r-a4base")
-    (version "1.44.0")
+    (version "1.46.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "a4Base" version))
        (sha256
         (base32
-         "15zqirz16gpks9f5d3d76h85b936za2jih74vfr55l5arqrrvvsn"))))
+         "14diri7gswd6h5p3bdhh20fy7i54d270mq985qcdvdyhx4kpw6g6"))))
     (properties `((upstream-name . "a4Base")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9712,14 +11826,14 @@ Affymetrix arrays.")
 (define-public r-a4
   (package
     (name "r-a4")
-    (version "1.44.0")
+    (version "1.46.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "a4" version))
        (sha256
         (base32
-         "1zs8fs6mdd7fhsmx4k824mid0jk400cm6dwfhl8z5lg85y8y2n0r"))))
+         "1sis4hwrxyn2x96yysz82gffl2kkj68ry945y15zwikwk80s31hb"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-a4base r-a4classif r-a4core r-a4preproc r-a4reporting))
@@ -9733,14 +11847,14 @@ Affymetrix arrays.")
 (define-public r-abseqr
   (package
     (name "r-abseqr")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "abseqR" version))
        (sha256
         (base32
-         "0jh3rj6ag07vpw6fymqm6m4jkrm9mgf50zkjncahxdf52mna8a9b"))))
+         "1z5an4vsm55a0qr46qmp8562vc3xdam5f3840r8hcdnn5dvzw414"))))
     (properties `((upstream-name . "abseqR")))
     (build-system r-build-system)
     (inputs
@@ -9781,14 +11895,14 @@ further downstream analysis on its output.")
 (define-public r-bacon
   (package
     (name "r-bacon")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bacon" version))
        (sha256
         (base32
-         "1zvcxdj3r892898ik5gq3jdbfig1438qws4bwd465ik8vi7g39v8"))))
+         "1v5kvvbc5fwvs84d2aq6gq6f6z0l68n7626gcnc8mh3sc27lxz53"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biocparallel r-ellipse r-ggplot2))
@@ -9806,14 +11920,14 @@ fitting a three-component normal mixture on z-scores.")
 (define-public r-rgadem
   (package
     (name "r-rgadem")
-    (version "2.44.0")
+    (version "2.46.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "rGADEM" version))
        (sha256
         (base32
-         "013xdwz0c3n0n9hxf8kkx570qry961pgdjsp023531pl5ww2ing4"))))
+         "070i3jdq8b5w7k42xw2fc3vcmv312i19fa1am4fbk3g3ssnm61p3"))))
     (properties `((upstream-name . "rGADEM")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9860,12 +11974,12 @@ distributions, modules and filter motifs.")
 (define-public r-motifdb
   (package
    (name "r-motifdb")
-   (version "1.38.0")
+   (version "1.40.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "MotifDb" version))
             (sha256
-             (base32 "1cyfz0l0yvdii3idaiq5w39yzxlzfpifa4v5pv7hdjfjj83a8rbi"))))
+             (base32 "122ifxmbi0v3192cd9chq265i3dyw3hzwsndq3w97f4d68vll7gl"))))
    (properties `((upstream-name . "MotifDb")))
    (build-system r-build-system)
    (propagated-inputs
@@ -9887,12 +12001,12 @@ frequency matrices from nine public sources, for multiple organisms.")
 (define-public r-motifbreakr
   (package
    (name "r-motifbreakr")
-   (version "2.10.0")
+   (version "2.12.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "motifbreakR" version))
             (sha256
-             (base32 "0sad73jjx52qzp1fmygp6xqvaxwl5szi69f00f94i1pdyq70qhlg"))))
+             (base32 "0lq79as9gb48hf3v2xj895s0nsjr37fqah4p405kdybzry56gvrq"))))
    (properties `((upstream-name . "motifbreakR")))
    (build-system r-build-system)
    (propagated-inputs
@@ -9937,14 +12051,14 @@ Bioconductor.")
 (define-public r-motifstack
   (package
     (name "r-motifstack")
-    (version "1.40.0")
+    (version "1.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "motifStack" version))
        (sha256
         (base32
-         "0d2ihx73chczbv6f91n04qb372plrdv7k4qws8shyw1fmvb1rq0z"))))
+         "18gfx5dq83s2ny39a7cgg4r3b05gg9l0kfg83brwrm1cby08jdhm"))))
     (properties `((upstream-name . "motifStack")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9969,14 +12083,14 @@ type and symbol colors.")
 (define-public r-genomicscores
   (package
     (name "r-genomicscores")
-    (version "2.8.2")
+    (version "2.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GenomicScores" version))
        (sha256
         (base32
-         "12rcxw69an1d5q7ar58xy8s871l47imw2nm08j054ivxslx8597j"))))
+         "1sz0gmwc5iam83pxnc702pd5h6nsa46kb0wsqs8ysb1ximbkfh5h"))))
     (properties `((upstream-name . "GenomicScores")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10007,14 +12121,14 @@ position-specific scores within R and Bioconductor.")
 (define-public r-atacseqqc
   (package
     (name "r-atacseqqc")
-    (version "1.20.2")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ATACseqQC" version))
        (sha256
         (base32
-         "0jj7n0mcj0gciw0ksazlksgmwzp51a40pwqhf0c7la0cc4bnrkqp"))))
+         "12ggi2dzf8qyzjrxprvk099f61yrabg2d84iqnjxzrn77v6z19b2"))))
     (properties `((upstream-name . "ATACseqQC")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10054,14 +12168,14 @@ footprints.")
 (define-public r-gofuncr
   (package
     (name "r-gofuncr")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GOfuncR" version))
        (sha256
         (base32
-         "02vdfsjrqp0m06mfbspwkxjyqxfca0w1idgygpi1a9i5m4fqhwpk"))))
+         "0d0xis4nns5icsr16w4ik2d95n3p2h93c47jvlp22crv7f4rlaa5"))))
     (properties `((upstream-name . "GOfuncR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10159,14 +12273,14 @@ different identifieres using the Biocore Data Team data-packages (e.g.
 (define-public r-annotationtools
   (package
     (name "r-annotationtools")
-    (version "1.70.0")
+    (version "1.72.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "annotationTools" version))
        (sha256
         (base32
-         "122b424zida3j0vqkn8d06sg3jpc3ngsgidr8kgg00n4cjngkc51"))))
+         "1z5vgblhi1kj2n9d4kbqgvwnm48372q0szgjshch8g39dypijvhd"))))
     (properties
      `((upstream-name . "annotationTools")))
     (build-system r-build-system)
@@ -10184,14 +12298,14 @@ text files).")
 (define-public r-allelicimbalance
   (package
     (name "r-allelicimbalance")
-    (version "1.34.0")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AllelicImbalance" version))
        (sha256
         (base32
-         "0w4xd0xzkwx7bbhrgqligpahlhg85rginknx520z891r8v0bim2z"))))
+         "0zn8pp4pl5wr957mf6agjpn61f9qpnjx0nbxb5wnbr40672x0263"))))
     (properties
      `((upstream-name . "AllelicImbalance")))
     (build-system r-build-system)
@@ -10227,14 +12341,14 @@ investigation using RNA-seq data.")
 (define-public r-aucell
   (package
     (name "r-aucell")
-    (version "1.18.1")
+    (version "1.20.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AUCell" version))
        (sha256
         (base32
-         "17wr7dycll0l1gax4w268qw7is163bs51rj6p1qnx1dgc9ibnsgr"))))
+         "1qb13qd5xzgrpx6jlg3ll0ff5spz3y06ji31vvqzm759almg2w3s"))))
     (properties `((upstream-name . "AUCell")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10243,6 +12357,7 @@ investigation using RNA-seq data.")
            r-delayedarray
            r-delayedmatrixstats
            r-gseabase
+           r-matrix
            r-mixtools
            r-r-utils
            r-shiny
@@ -10267,14 +12382,14 @@ needed.")
 (define-public r-ebimage
   (package
     (name "r-ebimage")
-    (version "4.38.0")
+    (version "4.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "EBImage" version))
        (sha256
         (base32
-         "1vcx45bw36k9daw9dywj5bz77jmqk4gjfwsym8ajjnc1jmlq20si"))))
+         "1k6gbivwlai451whq2vr3c0shzs9p4g188jn5waw7973gdzdi00q"))))
     (properties `((upstream-name . "EBImage")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10306,14 +12421,14 @@ visualization with image data.")
 (define-public r-yamss
   (package
     (name "r-yamss")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "yamss" version))
        (sha256
         (base32
-         "1lcfxw73cxvpy3bnq28pxdy5128mpq5xklsa0mzxdjyqc4g55hy8"))))
+         "0bh06mncjrkihz2j29hasbipfl50x7393wshdcnlxrs5rrq73r0n"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biocgenerics
@@ -10339,14 +12454,14 @@ analysis.")
 (define-public r-gtrellis
   (package
     (name "r-gtrellis")
-    (version "1.28.0")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gtrellis" version))
        (sha256
         (base32
-         "1s4xczzv6hz2kyv32xgcq84540w75qr3f644w1s4c3kwxgyq2gff"))))
+         "09f20qam59iwr48g854b7ydbsbqy90mdy83i2i0am4gybv5isgqg"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-circlize r-genomicranges r-getoptlong r-iranges))
@@ -10365,14 +12480,14 @@ genomic categories and to add self-defined graphics in the plot.")
 (define-public r-somaticsignatures
   (package
     (name "r-somaticsignatures")
-    (version "2.32.0")
+    (version "2.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "SomaticSignatures" version))
        (sha256
         (base32
-         "1ydnp54laznzpi08s403kxhnr5nqhvm3iilaxlcdlz0ngxhm6vx6"))))
+         "0xyh4pwwbpa1bmamqdhp84qhjdc2qsxc43xgknjrrja24d06ji2j"))))
     (properties
      `((upstream-name . "SomaticSignatures")))
     (build-system r-build-system)
@@ -10404,14 +12519,14 @@ decomposition algorithms.")
 (define-public r-yapsa
   (package
     (name "r-yapsa")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "YAPSA" version))
        (sha256
         (base32
-         "1klqfif4sadkxw7agywk2ncvcdqsnfb1d6adnacdfdasr8abvhid"))))
+         "17yxzqvyaa423k0rskahlgqxcsi70flgsxniry3f4m8yvmghxxkz"))))
     (properties `((upstream-name . "YAPSA")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10453,14 +12568,14 @@ provided.")
 (define-public r-gcrma
   (package
     (name "r-gcrma")
-    (version "2.68.0")
+    (version "2.70.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gcrma" version))
        (sha256
         (base32
-         "13a8igr2b02gsa6n3437kb33wg6h7si82fmqi35dzpfzhvx0qf6d"))))
+         "0a3wjwjgjkpmfvgg0b4jc1rkwzsqrjbaziydjfnkll4rw9xcavy1"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-affy
@@ -10535,14 +12650,14 @@ chips with the MAQC reference datasets.")
 (define-public r-quantro
   (package
     (name "r-quantro")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "quantro" version))
        (sha256
         (base32
-         "1zfrz7lxyrbf0c8d277npzj1h4six9whkqplvcjmn3li0xj5qng3"))))
+         "0f274wh0w6nyipac05y6s2m2p60vkls5j4fwa5bc419j68h4znnz"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase
@@ -10568,14 +12683,14 @@ groups.")
 (define-public r-yarn
   (package
     (name "r-yarn")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "yarn" version))
        (sha256
         (base32
-         "0z5202pqq02fwm8qf1g36004k7sv668s1xacbpr1cvw5sl452lbg"))))
+         "0sqbll7ja0qr8r28dqmydmkvg4ijfm7z8hbrsrz3xxdan70bmd2r"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase
@@ -10605,14 +12720,14 @@ large RNA-seq experiments.")
 (define-public r-roar
   (package
     (name "r-roar")
-    (version "1.32.0")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "roar" version))
        (sha256
         (base32
-         "0zq1praf5h9294cvmrb06l3chx8v40xw2sfvhlnh1516x9sjkwfc"))))
+         "1bf3ii3zaxkzw5y1wc5c474bq4cgavb67df54czmd3zi1lbhzphd"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biocgenerics
@@ -10673,14 +12788,14 @@ genes.")
 (define-public r-massspecwavelet
   (package
     (name "r-massspecwavelet")
-    (version "1.62.0")
+    (version "1.64.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MassSpecWavelet" version))
        (sha256
         (base32
-         "0g9izdy3f7h1zmsfbq45ahdz0ak5013rp3vxc4ijb1mpqx8ldd39"))))
+         "0l86gwq073nbx973v99b0lr9cz0pb72c4asmgj5w16jykicrnxn9"))))
     (properties
      `((upstream-name . "MassSpecWavelet")))
     (build-system r-build-system)
@@ -10697,14 +12812,14 @@ based on @dfn{Continuous Wavelet Transform} (CWT).")
 (define-public r-xcms
   (package
     (name "r-xcms")
-    (version "3.18.0")
+    (version "3.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "xcms" version))
        (sha256
         (base32
-         "0p2zd2728lj5q8y24gdfvsjijd6zl2i73hrcf017n32jq7vn71xm"))))
+         "1gj0nd90c6ykwn1n7xndzrgfv5dzy0y2lh3bf8120nacccgxl2qx"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase
@@ -10738,13 +12853,13 @@ data for high-throughput, untargeted analyte profiling.")
 (define-public r-wppi
   (package
     (name "r-wppi")
-    (version "1.4.0")
+    (version "1.6.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "wppi" version))
               (sha256
                (base32
-                "1008s39bb7sd261cy1vfgdah7bmhfw9qq322fh7g4wvpfw63ii9f"))))
+                "0kc3nkim8fhajhai5bwzwirsg74zbdib3dd7cfr75ddwd8myc913"))))
     (properties `((upstream-name . "wppi")))
     (build-system r-build-system)
     ;; This is necessary because omnipathr attempts to write a configuration
@@ -10779,14 +12894,14 @@ scores and a path search algorithm.")
 (define-public r-wrench
   (package
     (name "r-wrench")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Wrench" version))
        (sha256
         (base32
-         "1zx65s4m71wj85s2sq8ip54pq12r4sxfv8b2rxc41gfc5aj0zzca"))))
+         "0n7mvj9jdp8w5w64i49kkqzbrvpv2vzx6y6fb7g2sqp24wqrn39x"))))
     (properties `((upstream-name . "Wrench")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10803,14 +12918,14 @@ that arising from 16s metagenomic surveys.")
 (define-public r-wiggleplotr
   (package
     (name "r-wiggleplotr")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "wiggleplotr" version))
        (sha256
         (base32
-         "0s128mm5w8n072k6j0fv1mxnxjpwisjp5lpz8a9z96cnn69bnr0i"))))
+         "1yp9siy4249wkwd0yy5lkwp79xir53f8mihiv4dkir8fscgampl3"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-assertthat
@@ -10837,14 +12952,14 @@ visualization of exonic read coverage.")
 (define-public r-widgettools
   (package
     (name "r-widgettools")
-    (version "1.74.0")
+    (version "1.76.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "widgetTools" version))
        (sha256
         (base32
-         "10w1s5h4za6ibmphvj145ir3lp22qgah2z8fvmipmf8ciq1jf86d"))))
+         "1p93dzf7w9z1ria0f8n32aymam9abxyg50ngnh7s6a8n24mvvjy5"))))
     (properties `((upstream-name . "widgetTools")))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/widgetTools/")
@@ -10858,14 +12973,14 @@ widgets in R.")
 (define-public r-webbioc
   (package
     (name "r-webbioc")
-    (version "1.68.0")
+    (version "1.70.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "webbioc" version))
        (sha256
         (base32
-         "1g3srxsa2fqcn3r4wz4y19fwjmw3vawlcvdw6lbjdnvbgcafq1ah"))))
+         "1mgag0gjavpld4xxlpfafq6fhzjafxgqyf677xrm6ff26z6z1ja2"))))
     (build-system r-build-system)
     (inputs
      (list netpbm perl))
@@ -10890,14 +13005,14 @@ Currently only Affymetrix oligonucleotide analysis is supported.")
 (define-public r-zinbwave
   (package
     (name "r-zinbwave")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "zinbwave" version))
        (sha256
         (base32
-         "0vpz721sciw5b4ypxj5lj8p53gwkpfwlwkn6k3y8i65zg80p1g6i"))))
+         "1356ms5y6fg7ndn8hvs6zsyr0jg6ah7a56qxd2x4xgyjj3xcakbv"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biocparallel
@@ -10923,14 +13038,14 @@ the data.")
 (define-public r-zfpkm
   (package
     (name "r-zfpkm")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "zFPKM" version))
        (sha256
         (base32
-         "1h7g553rgb5mkmmsp8dyqqs9n9x17xmmcg3iijhb54nyrr2j1mji"))))
+         "1wsmv4fld4s7l0qh84ghizq8k388ybdz9hzzis2gn1nn57q1c7wi"))))
     (properties `((upstream-name . "zFPKM")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10948,14 +13063,14 @@ This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
 (define-public r-rbowtie2
   (package
     (name "r-rbowtie2")
-    (version "2.2.0")
+    (version "2.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rbowtie2" version))
        (sha256
         (base32
-         "0dhdx27vrkhd4fak0qb5q9amlcpi97xhf3ry39zk0ifx5zpjynkg"))))
+         "05cczwkhv7kfnhlr0qznk6vdjncaj907895923f8mwx4j4cy5gcz"))))
     (properties `((upstream-name . "Rbowtie2")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10975,14 +13090,14 @@ rapid adapter trimming, identification, and read merging.")
 (define-public r-progeny
   (package
     (name "r-progeny")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "progeny" version))
        (sha256
         (base32
-         "1rhy2l2yf9ndxlvff8756s6n8qyi42nz7a75lgygj5aqqckkj21b"))))
+         "0f5sfi9r9dr6w3xmspsbzby8dpza8x7djif7p2h6l99kwkf68jsb"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase
@@ -11007,14 +13122,14 @@ expression\".")
 (define-public r-arrmnormalization
   (package
     (name "r-arrmnormalization")
-    (version "1.36.0")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ARRmNormalization" version))
        (sha256
         (base32
-         "1pnvw8psbql787m8lrmhd9xbmgkc3dbc70yfds1aggv50dk3yjk1"))))
+         "14mffjsy7cwpa2xf8zdqwdk6mnfj3lf06y8s59ndh531b45nw5wc"))))
     (properties
      `((upstream-name . "ARRmNormalization")))
     (build-system r-build-system)
@@ -11030,14 +13145,14 @@ Infinium HumanMethylation 450k assay.")
 (define-public r-biocfilecache
   (package
     (name "r-biocfilecache")
-    (version "2.4.0")
+    (version "2.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocFileCache" version))
        (sha256
         (base32
-         "1bdbmlixrd8wvs25nmzdksq5hwnsxf8b6ds9qwx01h284vky5vsw"))))
+         "0skrvmkm6ch8gbpdi4wr59zk5vxzxs7cyqvz3jhki9d8w492wylg"))))
     (properties `((upstream-name . "BiocFileCache")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11063,14 +13178,14 @@ and data files used across sessions.")
 (define-public r-iclusterplus
   (package
     (name "r-iclusterplus")
-    (version "1.32.0")
+    (version "1.34.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "iClusterPlus" version))
        (sha256
         (base32
-         "0xzx3vly3p99zc5a69pra4jjp8d3bdhx7dl1l76w459cs58zy0sm"))))
+         "05y4jmbf8sxl32f3g5lw9ycxky0rw69gax3n2z0kif7xcb5qf3qv"))))
     (properties `((upstream-name . "iClusterPlus")))
     (build-system r-build-system)
     (native-inputs (list gfortran))
@@ -11093,14 +13208,14 @@ Gaussian distributions.")
 (define-public r-rbowtie
   (package
     (name "r-rbowtie")
-    (version "1.36.0")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rbowtie" version))
        (sha256
         (base32
-         "1ya1irwshsyy9l1fj51b04nv1ahq7a47ck7q19h2cly6yskc4x1q"))))
+         "1kbpqhidj2bwhp9gxqx2qjaby6fc2dfrnnyjkciswgxckis6h2pc"))))
     (properties `((upstream-name . "Rbowtie")))
     (build-system r-build-system)
     (arguments
@@ -11129,14 +13244,14 @@ alignment tool.")
 (define-public r-sgseq
   (package
     (name "r-sgseq")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "SGSeq" version))
        (sha256
         (base32
-         "0hz45367i70wl97silnimicdvs3g41zyf8syc6igz6471wbwkxwp"))))
+         "03ddz0mpgqqb52r7wa46bcr1ybf40126pg0n0n0pv6fnbq0ifwyc"))))
     (properties `((upstream-name . "SGSeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11172,14 +13287,14 @@ interpretation.")
 (define-public r-rhisat2
   (package
     (name "r-rhisat2")
-    (version "1.12.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rhisat2" version))
        (sha256
         (base32
-         "0hzair41l47kzykymd169a34pfhb98vrjgkgdf15m17csyz7pnv7"))))
+         "19dc9fadgl55icqc5xv834kigicxxr6cny83247jjbgf5zp16piv"))))
     (properties `((upstream-name . "Rhisat2")))
     (build-system r-build-system)
     (arguments
@@ -11210,14 +13325,14 @@ index.")
 (define-public r-quasr
   (package
     (name "r-quasr")
-    (version "1.36.0")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "QuasR" version))
        (sha256
         (base32
-         "1m0c0rdakkdn4rr6dh51c6rs40cbxkvz93n6s0m2kc6fqjv9zplf"))))
+         "1pp94368aj5wx0zcnbbm6zrxrfhixmbcdzpj2lka3blvq5j7sncj"))))
     (properties `((upstream-name . "QuasR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11252,14 +13367,14 @@ quantification of genomic regions of interest.")
 (define-public r-rqc
   (package
     (name "r-rqc")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rqc" version))
        (sha256
         (base32
-         "11j8m69zdcmpjb3xzr4s8sqmv8aqgl8q7k81gnd09l3nyjzy0h1k"))))
+         "02k64pjd1dlz5sksdbkbii9z4ihf1833ws7wwj81w3757zzabx0x"))))
     (properties `((upstream-name . "Rqc")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11295,14 +13410,14 @@ graphics.")
 (define-public r-birewire
   (package
     (name "r-birewire")
-    (version "3.28.0")
+    (version "3.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiRewire" version))
        (sha256
         (base32
-         "0r3i7n45qgj8wzdsx8wmfk0lc4xbcvxvmfziiqzig7r706q2c2hm"))))
+         "0nr40nm87qzbni3w0cik887csc899jh7j8z82i94v15fc30vfilh"))))
     (properties `((upstream-name . "BiRewire")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11348,14 +13463,14 @@ Markov-Chain-Monte-Carlo is applied to sample the activity states.")
 (define-public r-multidataset
   (package
     (name "r-multidataset")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MultiDataSet" version))
        (sha256
         (base32
-         "0rfs6jkzh1i4mj1pgfk4lwzmcl8pcwizra3q3282x3d8h2g98qnf"))))
+         "1qja5xd42wh8qbcil4hhnmh9zlby2gfglax2qbf5bzg3h6yzpy4g"))))
     (properties `((upstream-name . "MultiDataSet")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11385,19 +13500,21 @@ packages.")
 (define-public r-ropls
   (package
     (name "r-ropls")
-    (version "1.28.2")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ropls" version))
        (sha256
         (base32
-         "07gpx15r8c3wljiwxnff2zp7wxbhzz9r7njk8zg8hpy2q5qm3i6c"))))
+         "0vjwci0z83b56q1wi1k00926f0vh3220a44m0zzfxg2cm5j3fwxb"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase
+           r-ggplot2
            r-multiassayexperiment
            r-multidataset
+           r-plotly
            r-summarizedexperiment))
     (native-inputs
      (list r-knitr)) ; for vignettes
@@ -11425,14 +13542,14 @@ coefficients).")
 (define-public r-biosigner
   (package
     (name "r-biosigner")
-    (version "1.24.2")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biosigner" version))
        (sha256
         (base32
-         "0vdv2by3qv7y8vzr8qgg7apwwgsa0fhlfrhzns7g3nas7883c89m"))))
+         "11ncmxy4wqdg30w8a6dgcsywyzda49f9al435fz3pfj5rmlbbrlj"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase
@@ -11460,14 +13577,14 @@ datasets.")
 (define-public r-annotatr
   (package
     (name "r-annotatr")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "annotatr" version))
        (sha256
         (base32
-         "1fbax9v3d486c8lwf3yfjbf4w7zf53wmdpxk2clwm8ngm7w0pqm0"))))
+         "08f3xikgb0z1j7n8i04yn1dlfj8rxc76nmf5b7i5ljcp0jqiv07n"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotationdbi
@@ -11501,14 +13618,14 @@ annotations.")
 (define-public r-rsubread
   (package
     (name "r-rsubread")
-    (version "2.10.4")
+    (version "2.12.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rsubread" version))
        (sha256
         (base32
-         "155h25gbagqns7wpriil17li0jkdd1z1pcz0dlnikdqj4saf97rl"))))
+         "1gvd8vmglvzc3bixqxrm4k7yikl2as5l4x6bvvvnwsgx2i7vz7dm"))))
     (properties `((upstream-name . "Rsubread")))
     (build-system r-build-system)
     (inputs (list zlib))
@@ -11553,14 +13670,14 @@ and to both short and long sequence reads.")
 (define-public r-consensusclusterplus
   (package
     (name "r-consensusclusterplus")
-    (version "1.60.0")
+    (version "1.62.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ConsensusClusterPlus" version))
        (sha256
         (base32
-         "1021cix4mr9qsafskw4kk1l3wdzx9pk2gcwjifz6f4zqxss9v07p"))))
+         "15cz3bbl21vzf5xn5xb791sy2yvzir7h4fdqm0a5anhbh8jg0iaq"))))
     (properties
      `((upstream-name . "ConsensusClusterPlus")))
     (build-system r-build-system)
@@ -11619,14 +13736,14 @@ of the analyses while minimizing technical noise.")
 (define-public r-cytolib
   (package
     (name "r-cytolib")
-    (version "2.8.0")
+    (version "2.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "cytolib" version))
        (sha256
         (base32
-         "18b532sicca5l8sn334prrm7g1z1cakiwydccz4i833168pnsjyg"))))
+         "1y06x7z3p938kfvjx6zqab9hh1xzlrlhdxczyprx7lsd34ylz46n"))))
     (properties `((upstream-name . "cytolib")))
     (build-system r-build-system)
     (native-inputs
@@ -11648,24 +13765,24 @@ interact with gated cytometry data.")
 (define-public r-flowcore
   (package
     (name "r-flowcore")
-    (version "2.8.0")
+    (version "2.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowCore" version))
        (sha256
         (base32
-         "17nci6rc4i0vs0ibw5q8zy30ap7q4550qpq4ifkbblqbyzxlzkhr"))))
+         "0j0ryyz3vcih964is5gdm2jp39ssdli9q6r03q6rj9nwzplq5asj"))))
     (properties `((upstream-name . "flowCore")))
     (build-system r-build-system)
     (propagated-inputs
      (list r-bh
            r-biobase
            r-biocgenerics
+           r-cpp11
            r-cytolib
            r-matrixstats
            r-rcpp
-           r-rcpparmadillo
            r-rprotobuflib
            r-s4vectors))
     (native-inputs
@@ -11680,14 +13797,14 @@ with flow cytometry data.")
 (define-public r-flowmeans
   (package
     (name "r-flowmeans")
-    (version "1.56.0")
+    (version "1.58.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowMeans" version))
        (sha256
         (base32
-         "1n4li43ydwwf5gvgmdml4ba28cxymybg5wnz6jvp35n959fwxv6y"))))
+         "1hmr2i5svg1wvdgqhnp25k1c21p2pdd0ia9py5kp9sm5qvc9vngw"))))
     (properties `((upstream-name . "flowMeans")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11703,14 +13820,14 @@ change point detection.")
 (define-public r-ncdfflow
   (package
     (name "r-ncdfflow")
-    (version "2.42.0")
+    (version "2.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ncdfFlow" version))
        (sha256
         (base32
-         "18ba8rygcd1ys150pk38r4w5lxwm6sl76zkd294yg847dygsqa4m"))))
+         "0ak1rrd0r899nz4zdg9v3pkvlp94sbcc3q6xl249krgbx0a3sizm"))))
     (properties `((upstream-name . "ncdfFlow")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11734,14 +13851,14 @@ manipulation of flow cytometry data.")
 (define-public r-ggcyto
   (package
     (name "r-ggcyto")
-    (version "1.24.0")
+    (version "1.26.4")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ggcyto" version))
        (sha256
         (base32
-         "0sycyvdpa77mykzr709a7padh6478zmnzapibbq90qkc7bxnj359"))))
+         "1pj1v0bhvckvwn1p826phskqz9lv71c1913cz5w0fd87dzdbpzpj"))))
     (properties `((upstream-name . "ggcyto")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11771,14 +13888,14 @@ statistics to the plot.")
 (define-public r-flowviz
   (package
     (name "r-flowviz")
-    (version "1.60.0")
+    (version "1.62.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowViz" version))
        (sha256
         (base32
-         "175ygncrv6q6mb8pahixs89m9wm6hdpzx489gc9s8lgad2vrvz8f"))))
+         "0yz2b3l0bv5i7vrr893wrs3jl215i17m2hr92iisdc6mh9i0lpz8"))))
     (properties `((upstream-name . "flowViz")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11802,14 +13919,14 @@ statistics to the plot.")
 (define-public r-flowclust
   (package
     (name "r-flowclust")
-    (version "3.34.0")
+    (version "3.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowClust" version))
        (sha256
         (base32
-         "055vm9s8aha92znhpjqkipzprw8bkrinwjaik4ygmhym7w6vbblk"))))
+         "1l1lfgm6x06gyzda36m6gvqmb91zbrz8m83b1fnfzpxkhqha20yq"))))
     (properties `((upstream-name . "flowClust")))
     (build-system r-build-system)
     (arguments
@@ -11836,14 +13953,14 @@ model with Box-Cox transformation.")
 (define-public r-rprotobuflib
   (package
     (name "r-rprotobuflib")
-    (version "2.8.0")
+    (version "2.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RProtoBufLib" version))
        (sha256
         (base32
-         "1mvqwrm1y0vij66gdwgpf5l1h660wsi9jzjfs4ihw3zm4cb0q5pp"))))
+         "07d5skr8cp0hyjbs7whw4h8scrf2w4hyn0wzj3khqdss53zmmr2m"))))
     (properties `((upstream-name . "RProtoBufLib")))
     (build-system r-build-system)
     (arguments
@@ -11865,38 +13982,31 @@ for other R packages to compile and link against.")
 (define-public r-flowworkspace
   (package
     (name "r-flowworkspace")
-    (version "4.8.0")
+    (version "4.10.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowWorkspace" version))
        (sha256
         (base32
-         "0riyi9628cx1j5x6hmdd28yq75xh25j8ckcdz8dnb94dpvnhaqss"))))
+         "0jmbfclkfm0n2mshk94906kivii7awlskf7l7ydn8ki8wrpzxqg4"))))
     (properties `((upstream-name . "flowWorkspace")))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-aws-s3
-           r-aws-signature
-           r-bh
+     (list r-bh
            r-biobase
            r-biocgenerics
+           r-cpp11
            r-cytolib
            r-data-table
            r-delayedarray
-           r-digest
            r-dplyr
            r-flowcore
            r-ggplot2
            r-graph
-           r-lattice
-           r-latticeextra
            r-matrixstats
            r-ncdfflow
            r-rbgl
-           r-rcpp
-           r-rcpparmadillo
-           r-rcppparallel
            r-rgraphviz
            r-rhdf5lib
            r-rprotobuflib
@@ -11919,14 +14029,14 @@ matches the flowJo analysis.")
 (define-public r-flowstats
   (package
     (name "r-flowstats")
-    (version "4.8.0")
+    (version "4.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowStats" version))
        (sha256
         (base32
-         "1jbc92ah2mlpnd7v3k0207v4qz3rg9g9yy6r6y0s0cc5nifdyhwj"))))
+         "10xq0rfnshvam2yh34566ywmsby44aa1fg8wqwmllm202rhcgl2p"))))
     (properties `((upstream-name . "flowStats")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11957,38 +14067,30 @@ package.")
 (define-public r-opencyto
   (package
     (name "r-opencyto")
-    (version "2.8.0")
+    (version "2.10.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "openCyto" version))
        (sha256
         (base32
-         "1nz5fra0jf70jwyfbcz5ksnz5xb62vfnfwfasr0zwwvjvmmvrs1y"))))
+         "16wsa9dhnz8gz1siyhfxvnbfg142g7fmhxiqxr7n69qpq9w8yhr0"))))
     (properties `((upstream-name . "openCyto")))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-biobase
+     (list r-bh
+           r-biobase
            r-biocgenerics
-           r-clue
+           r-cpp11
            r-data-table
            r-flowclust
            r-flowcore
-           r-flowstats
            r-flowviz
            r-flowworkspace
            r-graph
-           r-gtools
-           r-ks
-           r-lattice
-           r-mass
            r-ncdfflow
-           r-plyr
-           r-r-utils
            r-rbgl
-           r-rcolorbrewer
-           r-rcpp
-           r-rrcov))
+           r-rcolorbrewer))
     (native-inputs
      (list r-knitr))
     (home-page "https://bioconductor.org/packages/openCyto")
@@ -12001,14 +14103,14 @@ sequential way to mimic the manual gating strategy.")
 (define-public r-cytoml
   (package
     (name "r-cytoml")
-    (version "2.8.0")
+    (version "2.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "CytoML" version))
        (sha256
         (base32
-         "0vp7advfh1d8596hjpzayasjhga4mx0l104sgz2asscbrjm4v7rr"))))
+         "105vdmwwglknwk7x7cb6b2jf6bngbxsly0ymjf8175p2lfv98jsa"))))
     (properties `((upstream-name . "CytoML")))
     (build-system r-build-system)
     (inputs
@@ -12053,14 +14155,14 @@ standard to exchange gated cytometry data with other software platforms.")
 (define-public r-flowsom
   (package
     (name "r-flowsom")
-    (version "2.4.0")
+    (version "2.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "FlowSOM" version))
        (sha256
         (base32
-         "0balsds5mm981cqamdjv3ndq1y9arharisd6f2lrpkzgvwawa645"))))
+         "1s7xilhhc55igq0zmvpfzhnh5df8bzmm3daknz75xhzhhg5b7z1c"))))
     (properties `((upstream-name . "FlowSOM")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12096,14 +14198,14 @@ self-organizing map clustering and minimal spanning trees.")
 (define-public r-mixomics
   (package
     (name "r-mixomics")
-    (version "6.20.0")
+    (version "6.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "mixOmics" version))
        (sha256
         (base32
-         "0fwc2w7frj0bjijzfckkxf7ipx1z13gw7907q4zr5qfl9mh127w7"))))
+         "0w6shihvnvkjycba1hy8drd8wcxxcl2rimkrb4vdl8aygdifrarx"))))
     (properties `((upstream-name . "mixOmics")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12142,14 +14244,14 @@ delete entire rows with missing data.")
 (define-public r-depecher
   (package                              ;Source/Weave error
     (name "r-depecher")
-    (version "1.12.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DepecheR" version))
        (sha256
         (base32
-         "0rixczdds5gpac50wap6s68kmpdj4208l38gcihkrysz5frbvqjp"))))
+         "1j4gxgw1s3a0nm888k02qi1smxqsplc42827ks666md025h9bxcj"))))
     (properties `((upstream-name . "DepecheR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12188,14 +14290,14 @@ data, to only emphasize the data that actually matters.")
 (define-public r-rcistarget
   (package
     (name "r-rcistarget")
-    (version "1.16.0")
+    (version "1.18.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RcisTarget" version))
        (sha256
         (base32
-         "17fnjkg6rjqj33v7slg81skqag10y6dc14g5iv69gqshjal4w4im"))))
+         "02lz2m2zhwy1dvmjvlss6qg0dh574qhnvn7al3wx7ck1hkz0dgi2"))))
     (properties `((upstream-name . "RcisTarget")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12230,14 +14332,14 @@ genes in the gene-set that are ranked above the leading edge).")
 (define-public r-chicago
   (package
     (name "r-chicago")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Chicago" version))
        (sha256
         (base32
-         "13vzxmvxpc3r9gii37zvhhr5nbnaggrva97g6m2n02qn9daf6vmm"))))
+         "1b24iiy6d5kzpixgpdkg4s1cb50jdrmgn9sjgvwr1qinckwz6zdn"))))
     (properties `((upstream-name . "Chicago")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12276,14 +14378,14 @@ expression space.")
 (define-public r-cicero
   (package
     (name "r-cicero")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "cicero" version))
        (sha256
         (base32
-         "1ip12ijazlmcfbym078slxykpkz7d1zwvs8l8aqdnqpxjfk1ipx5"))))
+         "0grzp9k06dz04bw07nf9qka19mara1kplyd24y8mg8208wk949f6"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-assertthat
@@ -12343,14 +14445,14 @@ accessibility data.")
 (define-public r-circrnaprofiler
   (package
     (name "r-circrnaprofiler")
-    (version "1.10.0")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "circRNAprofiler" version))
        (sha256
         (base32
-         "1gwm416shhv2p3gh1n6kv1rvx0n0imy25b7z62z4s8b3gs3nfp5j"))))
+         "07l8vaqbw36hvs8pyn1gk6dglnmkcmbafvd4rdrhg2wqwnlpsf40"))))
     (properties
      `((upstream-name . "circRNAprofiler")))
     (build-system r-build-system)
@@ -12478,14 +14580,14 @@ cisTopics and explore the nature and regulatory proteins driving them.")
 (define-public r-genie3
   (package
     (name "r-genie3")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GENIE3" version))
        (sha256
         (base32
-         "0h3vnpnznb9rda8gfwp4cnd2mqsvs1vzmfx90dchn5pqaphz1k2l"))))
+         "096crx7n75x60s9sx3l7nld3yvrsqs0clvjsdarxc6bbn2qxk81i"))))
     (properties `((upstream-name . "GENIE3")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12502,14 +14604,14 @@ regulatory networks from expression data.")
 (define-public r-roc
   (package
     (name "r-roc")
-    (version "1.72.0")
+    (version "1.74.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ROC" version))
        (sha256
         (base32
-         "0yfq0d0j2bzqdnjs6l2h6p48kmv9wfphlqym3brgndlnadipq1v2"))))
+         "00pw6xmxjzprbx8wskq6gbyqkfak764vic5yxrzs6wpram352vmv"))))
     (properties `((upstream-name . "ROC")))
     (build-system r-build-system)
     (native-inputs
@@ -12524,14 +14626,14 @@ Characteristic} (ROC) curves, with a focus on micro arrays.")
 (define-public r-watermelon
   (package
     (name "r-watermelon")
-    (version "2.2.0")
+    (version "2.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "wateRmelon" version))
        (sha256
         (base32
-         "0adqyfabrvfcaj3mwp0rbqlcgpj92yb205cyhibbrs5gdr5ri4pv"))))
+         "0m8mra0jb6sgm13dagqn1pj81dha4dyj65xc6r2sh0yc3pyjb20h"))))
     (properties `((upstream-name . "wateRmelon")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12562,14 +14664,14 @@ metrics, with methods for objects produced by the @code{methylumi} and
 (define-public r-gdsfmt
   (package
     (name "r-gdsfmt")
-    (version "1.32.0")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gdsfmt" version))
        (sha256
         (base32
-         "1cdwyivgfc6yw5hj9b3j57wx55gckwhx6fwx2lvqynrjzjyzf3q0"))
+         "1ck3qq4vhjp6vvicpldr7d2rkpspp5albjkbqjbshnbq11fhrk06"))
        (modules '((guix build utils)))
        ;; Remove bundled sources of zlib, lz4, and xz.  Don't attempt to build
        ;; them and link with system libraries instead.
@@ -12618,14 +14720,14 @@ with multiple R processes supported by the package @code{parallel}.")
 (define-public r-bigmelon
   (package
     (name "r-bigmelon")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bigmelon" version))
        (sha256
         (base32
-         "1msch4qbifkdqv0bbw03xj6d9w28z91mf4ki41rqg6048cq17h2k"))))
+         "094d43yv8af8sijp43ndcaincnsf3ng32vgwh6bfazlq5d601r6y"))))
     (properties `((upstream-name . "bigmelon")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12649,14 +14751,14 @@ with multiple R processes supported by the package @code{parallel}.")
 (define-public r-seqbias
   (package
     (name "r-seqbias")
-    (version "1.44.0")
+    (version "1.46.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "seqbias" version))
        (sha256
         (base32
-         "085nq6pf0bdn17wsbr5jnyy512v7rf67xff9rp5wz47mcifbv6rg"))))
+         "0mc6lv7vkch138n46gk1q1hfhv37mfxjij39q36wa0jy7s8cagfa"))))
     (properties `((upstream-name . "seqbias")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12673,14 +14775,14 @@ genome sequence.")
 (define-public r-reqon
   (package
     (name "r-reqon")
-    (version "1.42.0")
+    (version "1.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ReQON" version))
        (sha256
         (base32
-         "1f5pplm8fy3wvl0b6n18gph4dq9i9x5qiyjrj0bk0kwlkbpba74r"))))
+         "1r4dzwnqv6a4zy5q9l3axqq23sbk9pjfb2y3fmwxjvdwq6c1qnp0"))))
     (properties `((upstream-name . "ReQON")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12696,14 +14798,14 @@ format.")
 (define-public r-wavcluster
   (package
     (name "r-wavcluster")
-    (version "2.30.0")
+    (version "2.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "wavClusteR" version))
        (sha256
         (base32
-         "04di095i9i19j9ppx8gdsk7n18vd02d4rjdi9d4a3p0xv05ihnb6"))))
+         "1z7y3wnrqr2xqrvs2xwmv419aqlizq0az17dpxmj1hg9knyls1bx"))))
     (properties `((upstream-name . "wavClusteR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12784,14 +14886,14 @@ provides methods for retrieving enriched pathways.")
 (define-public r-variantfiltering
   (package
     (name "r-variantfiltering")
-    (version "1.32.0")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "VariantFiltering" version))
        (sha256
         (base32
-         "1bjqn8qik221x0bqvgd99p87v45iihwp6cxckh4ks964pd0c1xk8"))))
+         "110db9gcla796mbll3pin0hv2qp8r6khx0zzqfgzkp4mcyjxi62y"))))
     (properties
      `((upstream-name . "VariantFiltering")))
     (build-system r-build-system)
@@ -12890,14 +14992,14 @@ arrays based on fast wavelet-based functional models.")
 (define-public r-variancepartition
   (package
     (name "r-variancepartition")
-    (version "1.26.0")
+    (version "1.28.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "variancePartition" version))
        (sha256
         (base32
-         "0wk1xql8b0gxyrqz9hs54xvmp7qdw9b8jnv88p4vgv061iwyk7wv"))))
+         "0ypw3ckaf4qll83rl2bjzfc7g2m4v0n2mq645ppyfga8wv8kwssy"))))
     (properties
      `((upstream-name . "variancePartition")))
     (build-system r-build-system)
@@ -12918,6 +15020,7 @@ arrays based on fast wavelet-based functional models.")
            r-pbkrtest
            r-progress
            r-rdpack
+           r-remacor
            r-reshape2
            r-rhpcblasctl
            r-rlang
@@ -12938,14 +15041,14 @@ measures.")
 (define-public r-htqpcr
   (package
     (name "r-htqpcr")
-    (version "1.50.0")
+    (version "1.52.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "HTqPCR" version))
        (sha256
         (base32
-         "0am98rzwpi3kybq1l27c5qn3n1pg5aqwmh6jq9q0lzbjjin3haqc"))))
+         "1kclvh8f2sf534cjw07ry9nx74n6p7r0vmc3mk2nr37yvpf26b3q"))))
     (properties `((upstream-name . "HTqPCR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12968,14 +15071,14 @@ features (e.g.  genes, microRNAs).")
 (define-public r-unifiedwmwqpcr
   (package
     (name "r-unifiedwmwqpcr")
-    (version "1.32.0")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "unifiedWMWqPCR" version))
        (sha256
         (base32
-         "1skfs94a6bv05c844zf5vfqw1fbgxyppgdnckdbhxg2a2470a4wh"))))
+         "0zkqr1s8gagwsh33kzp0n2n7ff5jhfn6a60gvab5spk7vr76j442"))))
     (properties
      `((upstream-name . "unifiedWMWqPCR")))
     (build-system r-build-system)
@@ -12992,14 +15095,14 @@ data.")
 (define-public r-universalmotif
   (package
     (name "r-universalmotif")
-    (version "1.14.1")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "universalmotif" version))
        (sha256
         (base32
-         "1sm54z8aq3534qjsa19wychhwcvwnjlkydmiqqvidiiwcxwqpjsr"))))
+         "1vfg703wxbgxw2cwqqz3kfyqj4za5n3skxxzi8c31azamg4hxs18"))))
     (properties
      `((upstream-name . "universalmotif")))
     (build-system r-build-system)
@@ -13040,13 +15143,13 @@ motifs, and others.")
 (define-public r-ace
   (package
     (name "r-ace")
-    (version "1.14.0")
+    (version "1.16.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "ACE" version))
               (sha256
                (base32
-                "1xnw288vz810vjkidar5h218wyc0q2hx0k4zi3r88vaz5rfhc05m"))))
+                "12gmdkzm9wnrq793xqvw3mzwmmsm1vkh36llapr7m7q4dmcfgxr0"))))
     (properties `((upstream-name . "ACE")))
     (build-system r-build-system)
     (propagated-inputs (list r-biobase r-genomicranges r-ggplot2 r-qdnaseq))
@@ -13069,13 +15172,13 @@ of @dfn{tumor cells} (cells with divergent segments).")
 (define-public r-acgh
   (package
     (name "r-acgh")
-    (version "1.74.0")
+    (version "1.76.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "aCGH" version))
               (sha256
                (base32
-                "00ni0kwy68v33ggfi8g5vffirhmbhaxg4l54hcqhx75m535z1x7d"))))
+                "05q303bf8acvhbdzqxqk2gf12vg0fdqknlxryn2cs8nijx40zp46"))))
     (properties `((upstream-name . "aCGH")))
     (build-system r-build-system)
     (propagated-inputs (list r-biobase r-cluster r-multtest r-survival))
@@ -13093,13 +15196,13 @@ printing and plotting @code{aCGH} objects.")
 (define-public r-acme
   (package
     (name "r-acme")
-    (version "2.52.0")
+    (version "2.54.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "ACME" version))
               (sha256
                (base32
-                "0ilcsgpc4m47gifxc0yzx2xi3g4day515mncnnjvfdj3iq8xwk25"))))
+                "0prcaxqmzm4hhpv228xh0glhm166gs17sa9h4lqrm03pwrjrdqdw"))))
     (properties `((upstream-name . "ACME")))
     (build-system r-build-system)
     (propagated-inputs (list r-biobase r-biocgenerics))
@@ -13120,13 +15223,13 @@ on whole-genome tiling array experiments quite easily with enough memory.")
 (define-public r-acde
   (package
     (name "r-acde")
-    (version "1.26.0")
+    (version "1.28.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "acde" version))
               (sha256
                (base32
-                "0lgq546y4qklfzbc6fjr3d656hn76p6dn4694qfiafql2nlsjbj2"))))
+                "1d47hbna68qm517afk1wb0w9gb8j52p7nqh5axcc6h76zppsc1sp"))))
     (properties `((upstream-name . "acde")))
     (build-system r-build-system)
     (propagated-inputs (list r-boot))
@@ -13213,14 +15316,14 @@ cellular organization in health and disease.")
 (define-public r-bgmix
   (package
     (name "r-bgmix")
-    (version "1.56.0")
+    (version "1.58.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BGmix" version))
        (sha256
         (base32
-         "03f6nknp3n49yvg2d9qsmds676rva70pr4wjz0md228jczgjk0vj"))))
+         "0r4cxrjvf3qr5514lsw1s53h4by3djb9ipkz7bi979w343dn9xfx"))))
     (properties `((upstream-name . "BGmix")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13235,14 +15338,14 @@ gene expression.")
 (define-public r-bgx
   (package
     (name "r-bgx")
-    (version "1.62.0")
+    (version "1.64.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bgx" version))
        (sha256
         (base32
-         "0q2y4n6bcc9pvz5sgfkw1lrb00rrp7q29i1vh7srdfmfhgpyz6bk"))))
+         "1ylg9bnq8iwax0ap4c19v4mkbq673s8dfv49d94znsryg3fp93dl"))))
     (properties `((upstream-name . "bgx")))
     (build-system r-build-system)
     (arguments
@@ -13271,14 +15374,14 @@ Affymetrix GeneChips.")
 (define-public r-bhc
   (package
     (name "r-bhc")
-    (version "1.48.0")
+    (version "1.50.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BHC" version))
        (sha256
         (base32
-         "1kqajd16981y5yaak2imaq1i7pilgqdr3nbhggsakh787j1d9rc5"))))
+         "0ryd9lg8pywqlxj802y9jad5nxy40ivnzdq2ldldypwyalgk9ahm"))))
     (properties `((upstream-name . "BHC")))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/BHC/")
@@ -13297,14 +15400,14 @@ algorithm which is more efficient for larger data sets.")
 (define-public r-bicare
   (package
     (name "r-bicare")
-    (version "1.54.0")
+    (version "1.56.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BicARE" version))
        (sha256
         (base32
-         "0qjh5bsjcjry6k1vzdaascwy2shjrkc2bw0w57w0qa458cbi89z2"))))
+         "1z7x30705a4ww9vdam2668pk064na5ispigqnaqy8zqvlfvp3c8d"))))
     (properties `((upstream-name . "BicARE")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13319,14 +15422,14 @@ results.")
 (define-public r-bifet
   (package
     (name "r-bifet")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiFET" version))
        (sha256
         (base32
-         "03ypbbn8i0f4bl4m6wfdcv702jydniak56wqjb1vlrckd9aphwzq"))))
+         "0awzq3i7ga6jsh7xgmrpzz8klx69p8cxj73p6h7ya43bgcr0iff0"))))
     (properties `((upstream-name . "BiFET")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13348,14 +15451,14 @@ the read count and GC content bias.")
 (define-public r-rsbml
   (package
     (name "r-rsbml")
-    (version "2.54.0")
+    (version "2.56.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "rsbml" version))
        (sha256
         (base32
-         "1v11pspkml6xdsacgwxw8r4qdhbnn2h2sqgpm9aidaq9p2085b0v"))))
+         "1syg49qz6vwzyw2zrxwrfb7kzgk0lim1q674f7mfvjah1fnv8bgc"))))
     (properties `((upstream-name . "rsbml")))
     (build-system r-build-system)
     (inputs
@@ -13374,14 +15477,14 @@ validating output, provides an S4 SBML DOM, converts SBML to R graph objects.")
 (define-public r-hypergraph
   (package
     (name "r-hypergraph")
-    (version "1.68.0")
+    (version "1.70.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "hypergraph" version))
        (sha256
         (base32
-         "0xmryqj5yw1ns6wbhjqbb6h14jlj89zrznzvqnvd4n03ci20kzzp"))))
+         "1jvnvzjivjwqxh19c3g37kpyl6i6mxw99ma3ypjjgxzx898nsg45"))))
     (properties `((upstream-name . "hypergraph")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13396,14 +15499,14 @@ manipulating hypergraphs.")
 (define-public r-hyperdraw
   (package
     (name "r-hyperdraw")
-    (version "1.48.0")
+    (version "1.50.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "hyperdraw" version))
        (sha256
         (base32
-         "0ndw4y6b15jy4w86vfkahmdc81d3ycjsvqy1mxi55dwvd8xq0ap6"))))
+         "1fl4ia2jskvmbwk0y1wd0x4dgqph0av7bx2zffrvd1a5ppcjmsra"))))
     (properties `((upstream-name . "hyperdraw")))
     (build-system r-build-system)
     (inputs (list graphviz))
@@ -13418,14 +15521,14 @@ manipulating hypergraphs.")
 (define-public r-biggr
   (package
     (name "r-biggr")
-    (version "1.32.0")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiGGR" version))
        (sha256
         (base32
-         "0n57bgl6xz5b1gpw4isimq2pqxmlabn7jzhbjg2fbxcklabdvrcw"))))
+         "07b80qpkbas3x2yhndcm6vdkba0cpricyvnjf18dxklj5j612wfy"))))
     (properties `((upstream-name . "BiGGR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13482,14 +15585,14 @@ a file-backed matrix with factor properties.")
 (define-public r-bigpint
   (package
     (name "r-bigpint")
-    (version "1.12.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bigPint" version))
        (sha256
         (base32
-         "1hp69j2qcidrxqs3dxjjngb09nbzp5x2yy4jz1rjmv6ghif9ccfj"))))
+         "1smf3w5a60jc0bpip5131ad9ykmnrcd33qi3pc3m50g6kn023wz2"))))
     (properties `((upstream-name . "bigPint")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13525,14 +15628,14 @@ visualizing RNA-sequencing datasets and differentially expressed genes.")
 (define-public r-chemminer
   (package
     (name "r-chemminer")
-    (version "3.48.0")
+    (version "3.50.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChemmineR" version))
        (sha256
         (base32
-         "1nri4zkc9lp1mqgsi0h58486vixwiv2989b6pmx2aj5c3575i0ma"))))
+         "0rk4ydanqxjh5yj0m9qlj06a12j7rkx9gxv6x7zpiyvnscahw63i"))))
     (properties `((upstream-name . "ChemmineR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13568,13 +15671,13 @@ structures.")
 (define-public r-fmcsr
   (package
     (name "r-fmcsr")
-    (version "1.38.0")
+    (version "1.40.0")
     (source
       (origin
         (method url-fetch)
         (uri (bioconductor-uri "fmcsR" version))
         (sha256
-          (base32 "1mblmk21dxc9v2fikhvfg2njwgl190gkysppl6msxizwcmxsmh30"))))
+          (base32 "00xi01wz61ip8pnbrpnpp8hncb8gyiw69qkbg0cl425rv6qjb3mr"))))
     (properties `((upstream-name . "fmcsR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13597,14 +15700,14 @@ searching and clustering.")
 (define-public r-bioassayr
   (package
     (name "r-bioassayr")
-    (version "1.34.0")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bioassayR" version))
        (sha256
         (base32
-         "0zbrci0vgk4qca28i0qb2izhyrz3r95l1w54h9h3zj9f3vd61wrz"))))
+         "0r56r4qxibgblriyfbd46i8jhc2bfr9ndr8i30920v9kc3n83cav"))))
     (properties `((upstream-name . "bioassayR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13632,14 +15735,14 @@ available bioactivity data.")
 (define-public r-biobroom
   (package
     (name "r-biobroom")
-    (version "1.28.0")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biobroom" version))
        (sha256
         (base32
-         "04x1z9nchm4mbhqr31011zdprc4md156j4zf003s7xx0n278xsgh"))))
+         "02gdc26bs0yx7hb53b8ncipsaw6ynfvjcx64qxkxxq1c4awjkhzy"))))
     (properties `((upstream-name . "biobroom")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13661,18 +15764,18 @@ visualize bioinformatics analyses.")
 (define-public r-graphite
   (package
     (name "r-graphite")
-    (version "1.42.0")
+    (version "1.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "graphite" version))
        (sha256
         (base32
-         "0nl5mkgrvf7vsqjy48ij9b1dmxfvp9lf8cpay55h93c4qz4x606g"))))
+         "0gkjab12ncag1vslc5bwlr0m5ac3ifq9ka5nfq7ckrpns98s7k0w"))))
     (properties `((upstream-name . "graphite")))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-annotationdbi r-graph r-httr r-rappdirs r-rlang))
+     (list r-annotationdbi r-graph r-httr r-purrr r-rappdirs r-rlang))
     (home-page "https://bioconductor.org/packages/graphite/")
     (synopsis "Networks from pathway databases")
     (description
@@ -13684,14 +15787,14 @@ symbols).")
 (define-public r-reactomepa
   (package
     (name "r-reactomepa")
-    (version "1.40.0")
+    (version "1.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ReactomePA" version))
        (sha256
         (base32
-         "1fd72m2afxbbvbgwy8knp6fiq1h561plmsh4r8a08w21ngmkz2s5"))))
+         "06994hk9nrzlgz8sby61656rdbf1r954v71djl1i7141dgw5rif2"))))
     (properties `((upstream-name . "ReactomePA")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13701,6 +15804,7 @@ symbols).")
            r-ggplot2
            r-ggraph
            r-graphite
+           r-gson
            r-igraph
            r-reactome-db))
     (native-inputs
@@ -13716,14 +15820,14 @@ enrichment analysis and several functions for visualization.")
 (define-public r-ebarrays
   (package
     (name "r-ebarrays")
-    (version "2.60.0")
+    (version "2.62.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "EBarrays" version))
        (sha256
         (base32
-         "027zarnpxpdnyl877swp5ypxj7zvq0cjp2q2xs6g6yn5dpqjvxxk"))))
+         "0kg22appd9sd6knm129hchkamzilwr3h8wi4ibrvllbfmx31v9q8"))))
     (properties `((upstream-name . "EBarrays")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13735,6 +15839,28 @@ enrichment analysis and several functions for visualization.")
 microarray data.")
     (license license:gpl2+)))
 
+(define-public r-biocbaseutils
+  (package
+    (name "r-biocbaseutils")
+    (version "1.0.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "BiocBaseUtils" version))
+              (sha256
+               (base32
+                "0p6siidrx8q6qr36fc67hzi091m2zwik3zngj27yllbfz6sn5k69"))))
+    (properties `((upstream-name . "BiocBaseUtils")))
+    (build-system r-build-system)
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/BiocBaseUtils")
+    (synopsis "General utility functions for developing Bioconductor packages")
+    (description
+     "The package provides utility functions related to package development.
+These include functions that replace slots, and selectors for show methods.
+It aims to coalesce the various helper functions often re-used throughout the
+Bioconductor ecosystem.")
+    (license license:artistic2.0)))
+
 (define-public r-bioccasestudies
   (package
     (name "r-bioccasestudies")
@@ -13760,13 +15886,13 @@ monograph.")
 (define-public r-bioccheck
   (package
     (name "r-bioccheck")
-    (version "1.32.0")
+    (version "1.34.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocCheck" version))
               (sha256
                (base32
-                "1k1gxzmxx26hmwdxgagv93mv4jwyygkk8703ds6nvryzhqffzkbc"))))
+                "1zj43kbzvi2ws8c182fp6vn5r6iiqsr6p2iyy3k8n3ifm2acqw2h"))))
     (properties
      `((upstream-name . "BiocCheck")))
     (build-system r-build-system)
@@ -13789,14 +15915,14 @@ checks on R packages that are to be submitted to the Bioconductor repository.")
 (define-public r-biocgraph
   (package
     (name "r-biocgraph")
-    (version "1.58.0")
+    (version "1.60.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biocGraph" version))
        (sha256
         (base32
-         "1y59a7c4ahhn1g2wz2hkx83izfn8i85mmxxp63jdd0rg7zwhr6nn"))))
+         "0ysdmv2hyl8jnmr42lkyvgfqb0z89f5p649ahx0ygs6fw0z226xa"))))
     (properties `((upstream-name . "biocGraph")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13811,13 +15937,13 @@ different graph related packages produced by Bioconductor.")
 (define-public r-biocstyle
   (package
     (name "r-biocstyle")
-    (version "2.24.0")
+    (version "2.26.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocStyle" version))
               (sha256
                (base32
-                "1nwiib201b9q1x19ihqjqr5jl0vnid8wfgpi8sa3y02bn722g5a5"))))
+                "092hpmyhra755j32vc8w2l6xqwg09jm8apnk5rvxi1cm5034yvsl"))))
     (properties
      `((upstream-name . "BiocStyle")))
     (build-system r-build-system)
@@ -13835,13 +15961,13 @@ functionality.")
 (define-public r-biocviews
   (package
     (name "r-biocviews")
-    (version "1.64.0")
+    (version "1.66.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "biocViews" version))
               (sha256
                (base32
-                "1lahla53awdqiglfiygbxg5pkzfabym7n5abgyp1nvqsvsj0g126"))))
+                "0fdxlixwf4d3p1prq37cgfvaiym44h2yd4bym6wp4dl8h648v99y"))))
     (properties
      `((upstream-name . "biocViews")))
     (build-system r-build-system)
@@ -13853,6 +15979,7 @@ functionality.")
            r-rcurl
            r-xml
            r-runit))
+    (native-inputs (list r-knitr))
     (home-page "https://bioconductor.org/packages/biocViews")
     (synopsis "Bioconductor package categorization helper")
     (description "The purpose of biocViews is to create HTML pages that
@@ -13863,14 +15990,14 @@ also known as views, in a controlled vocabulary.")
 (define-public r-experimenthub
   (package
     (name "r-experimenthub")
-    (version "2.4.0")
+    (version "2.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ExperimentHub" version))
        (sha256
         (base32
-         "11hna8vrm1az1zk7pw2dv0wh84sd0hw2bi55w40hqvs36csb7lkl"))))
+         "1j71zmxwiz82gg6kii2bmynzwll1r6fmsq972kmvxvm6crpvi15s"))))
     (properties `((upstream-name . "ExperimentHub")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13897,14 +16024,14 @@ access.")
 (define-public r-grohmm
   (package
     (name "r-grohmm")
-    (version "1.30.1")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "groHMM" version))
        (sha256
         (base32
-         "0v2mk7xcy483w2nygpmyjp73kj3v5pkk1kf1wr41n33dxqlddqai"))))
+         "1as3k6avyc4l7saw02x0ql68c06msvs1s824vc1xg6lkdsi4lsyc"))))
     (properties `((upstream-name . "groHMM")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13924,20 +16051,22 @@ access.")
 (define-public r-multiassayexperiment
   (package
     (name "r-multiassayexperiment")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MultiAssayExperiment" version))
        (sha256
         (base32
-         "1wnp52l9vifxn1wzqgndzp9b6ih0s1cflxx1fhw32k32d05cw9q1"))))
+         "00lhnqa4yz3lm5kl79bghad93iijihnassy2caf87czc540why09"))))
     (properties
      `((upstream-name . "MultiAssayExperiment")))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase
+           r-biocbaseutils
            r-biocgenerics
+           r-delayedarray
            r-genomicranges
            r-iranges
            r-s4vectors
@@ -13959,14 +16088,14 @@ rownames.")
 (define-public r-bioconcotk
   (package
     (name "r-bioconcotk")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocOncoTK" version))
        (sha256
         (base32
-         "1alplszw84vqa1mvzp996f94s40scmh4qwbrqhg43hrnyvbnq7pi"))))
+         "1x4mzzjvjgcxg5xyxjib8r2n55hpf2vzcci0xkb7d8frakfncn9s"))))
     (properties `((upstream-name . "BiocOncoTK")))
     (build-system r-build-system)
     (propagated-inputs
@@ -14004,14 +16133,14 @@ tools for genome-scale analysis of cancer studies.")
 (define-public r-biocor
   (package
     (name "r-biocor")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BioCor" version))
        (sha256
         (base32
-         "004mksswampwisljcdz6fswwbgdjdii3y86gjzib0gf8v4w7w4q3"))))
+         "0a8xyrmarb2ja5zyvx5sndd67hylmwi29gpr5lwrzinww8w8b8w6"))))
     (properties `((upstream-name . "BioCor")))
     (build-system r-build-system)
     (propagated-inputs
@@ -14031,14 +16160,14 @@ gene selection, testing relationships, and so on.")
 (define-public r-biocpkgtools
   (package
     (name "r-biocpkgtools")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocPkgTools" version))
        (sha256
         (base32
-         "1v0824vmg49q9lh0igdyniryyknw6vmh462rn25kmg9hdna0w99h"))))
+         "1av7vnw6z9cw7j4d3vpi8mfs5h4pn4yr2wc8ybg7ad1d686ah845"))))
     (properties `((upstream-name . "BiocPkgTools")))
     (build-system r-build-system)
     (propagated-inputs
@@ -14058,11 +16187,10 @@ gene selection, testing relationships, and so on.")
            r-rbgl
            r-readr
            r-rlang
+           r-rorcid
            r-rvest
            r-stringr
            r-tibble
-           r-tidyr
-           r-tidyselect
            r-xml2))
     (native-inputs
      (list r-knitr))
@@ -14079,14 +16207,14 @@ analytics on packages.")
 (define-public r-biocset
   (package
     (name "r-biocset")
-    (version "1.10.0")
+    (version "1.12.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocSet" version))
        (sha256
         (base32
-         "1ghba7020inrdxlbrrgds9gjymjxjma2p89b9lgkjin89zalqglh"))))
+         "1cqp5m6yic5vsp8k05r50sx2cmi9cwzxfmlswcjw28nascq3gpv0"))))
     (properties `((upstream-name . "BiocSet")))
     (build-system r-build-system)
     (propagated-inputs
@@ -14117,14 +16245,14 @@ accessing web references for elements/sets are also available in BiocSet.")
 (define-public r-biocworkflowtools
   (package
     (name "r-biocworkflowtools")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocWorkflowTools" version))
        (sha256
         (base32
-         "1jj4icpkhrv9f6yx3vghkpdil1pfghf3yvc9756wmndvhs100r5l"))))
+         "00cy5lqmfap57bm2s00bis9ddci2lv1lrp0mk5ydgx061p4ym29i"))))
     (properties
      `((upstream-name . "BiocWorkflowTools")))
     (build-system r-build-system)
@@ -14150,14 +16278,14 @@ Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.")
 (define-public r-biodist
   (package
     (name "r-biodist")
-    (version "1.68.0")
+    (version "1.70.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bioDist" version))
        (sha256
         (base32
-         "04nrvrcvpj0sn8p2i8n3ggsl2s7r4na576174i7bn1sj21vr0yb0"))))
+         "1fnx3q5arsilrvnhndplap8h4ydi9bvmlpfllj1li124hn5n2w3d"))))
     (properties `((upstream-name . "bioDist")))
     (build-system r-build-system)
     (propagated-inputs
@@ -14172,14 +16300,14 @@ distance measures.")
 (define-public r-pcatools
   (package
     (name "r-pcatools")
-    (version "2.8.0")
+    (version "2.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "PCAtools" version))
        (sha256
         (base32
-         "03s4dh008fys2rrcpzanc0892p63f6jyyvzc9m42jbi1dlkyx26v"))))
+         "1r32ajjmrhlwl0ylwavlfzph6m01mq3y7r87x8mbkmqw9ld1y2fd"))))
     (properties `((upstream-name . "PCAtools")))
     (build-system r-build-system)
     (propagated-inputs
@@ -14218,18 +16346,40 @@ dimensional mass cytometry data.")
 (define-public r-rgreat
   (package
     (name "r-rgreat")
-    (version "1.28.0")
+    (version "2.0.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "rGREAT" version))
        (sha256
         (base32
-         "0px72r8mjimf5mxfwb9qz46kqpgjw5gaqq41hy0212ymjd8whaky"))))
+         "1vmm7s5p8wqz1r8g1hy1l3mra3kkf76qgy5jkf84jxz7pi0clbld"))))
     (properties `((upstream-name . "rGREAT")))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-genomicranges r-getoptlong r-iranges r-rcurl r-rjson))
+     (list r-annotationdbi
+           r-circlize
+           r-digest
+           r-doparallel
+           r-dt
+           r-foreach
+           r-genomeinfodb
+           r-genomicfeatures
+           r-genomicranges
+           r-getoptlong
+           r-globaloptions
+           r-go-db
+           r-iranges
+           r-org-hs-eg-db
+           r-progress
+           r-rcolorbrewer
+           r-rcurl
+           r-rcpp
+           r-rjson
+           r-s4vectors
+           r-shiny
+           r-txdb-hsapiens-ucsc-hg19-knowngene
+           r-txdb-hsapiens-ucsc-hg38-knowngene))
     (native-inputs (list r-knitr))
     (home-page "https://github.com/jokergoo/rGREAT")
     (synopsis "Client for GREAT analysis")
@@ -14242,14 +16392,14 @@ user's input and automatically retrieving results from GREAT web server.")
 (define-public r-m3c
   (package
     (name "r-m3c")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "M3C" version))
        (sha256
         (base32
-         "120gd7gkgc98d1l6hl2ij799b3jksdnga5iyb44ps9mbc79hl012"))))
+         "1djgbnxsdp1w9hhc6346gmvad3x8avy8nc85gpvg9i4x52wcrn4j"))))
     (properties `((upstream-name . "M3C")))
     (build-system r-build-system)
     (propagated-inputs
@@ -14275,14 +16425,14 @@ hypothesis @code{K=1}.")
 (define-public r-icens
   (package
     (name "r-icens")
-    (version "1.68.0")
+    (version "1.70.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Icens" version))
        (sha256
         (base32
-         "0jnbfv7js8bw0ginql90krrpk0p54whj9igw0zk3jc45jqvj2vyc"))))
+         "13ygc467nqh0235sf1ags1ihv7pg2yriva6qi7z46c534vxv6b8n"))))
     (properties `((upstream-name . "Icens")))
     (build-system r-build-system)
     (propagated-inputs
@@ -14398,14 +16548,14 @@ generated.")
 (define-public r-preprocesscore
   (package
     (name "r-preprocesscore")
-    (version "1.58.0")
+    (version "1.60.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "preprocessCore" version))
        (sha256
         (base32
-         "1sqpp00hhv6gypflrjw8qpqyqgdcp29m86gmi1di1574x8casdkf"))))
+         "1rwr31jp4dh3xcfx1kx8rz5xvyx1mrwy85hqrjrfr4m6h0qv28k1"))))
     (properties
      `((upstream-name . "preprocessCore")))
     (build-system r-build-system)
@@ -14419,13 +16569,13 @@ routines.")
 (define-public r-s4vectors
   (package
     (name "r-s4vectors")
-    (version "0.34.0")
+    (version "0.36.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "S4Vectors" version))
               (sha256
                (base32
-                "0j3ybhzdhlhw8527nks3mjja28asjya2n0m0rjkh4bw66rkfys4k"))))
+                "16lssnmhy3klqp4sw1328f38cixkjh9317gdyikcrmsbcwg2ak6v"))))
     (properties
      `((upstream-name . "S4Vectors")))
     (build-system r-build-system)
@@ -14486,14 +16636,14 @@ data manipulation and visualization.")
 (define-public r-rgraphviz
   (package
     (name "r-rgraphviz")
-    (version "2.40.0")
+    (version "2.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rgraphviz" version))
        (sha256
         (base32
-         "1r6ff7w2bmyfl1vzjvpgnhb8f5arwjlpab8fw5ph8fgyiqbcx94l"))))
+         "0blymdax10zzg2lpj4hgvyh9c01b1qaivrc0gx95swji37zkqnwm"))))
     (properties `((upstream-name . "Rgraphviz")))
     (build-system r-build-system)
     (arguments
@@ -14521,16 +16671,54 @@ data manipulation and visualization.")
 objects from the @code{graph} package.")
     (license license:epl1.0)))
 
+(define-public r-fishpond
+  (package
+    (name "r-fishpond")
+    (version "2.4.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "fishpond" version))
+              (sha256
+               (base32
+                "112jd53wbiv1w0n8dc4qn6257wbbbg5i20s9wlvaw98jma94afa6"))))
+    (properties `((upstream-name . "fishpond")))
+    (build-system r-build-system)
+    (inputs (list zlib))
+    (propagated-inputs
+     (list r-abind
+           r-genomicranges
+           r-gtools
+           r-iranges
+           r-jsonlite
+           r-matrix
+           r-matrixstats
+           r-qvalue
+           r-rcpp
+           r-s4vectors
+           r-singlecellexperiment
+           r-summarizedexperiment
+           r-svmisc))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/mikelove/fishpond")
+    (synopsis "Downstream methods and tools for expression data")
+    (description
+     "The @code{fishpond} package contains methods for differential transcript
+and gene expression analysis of RNA-seq data using inferential replicates for
+uncertainty of abundance quantification, as generated by Gibbs sampling or
+bootstrap sampling.  Also the package contains a number of utilities for
+working with Salmon and Alevin quantification files.")
+    (license license:gpl2)))
+
 (define-public r-fithic
   (package
     (name "r-fithic")
-    (version "1.22.0")
+    (version "1.24.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "FitHiC" version))
               (sha256
                (base32
-                "0iv14yx3g7shzl8qrjknyxbmiylj51sbd1wzr1ff9lc5shgl55kq"))))
+                "1c7jscl82knbh5ha1i1hlm46nnhz6aw5h0j5xnl4hlgx8mnn05fl"))))
     (properties `((upstream-name . "FitHiC")))
     (build-system r-build-system)
     (propagated-inputs
@@ -14548,13 +16736,13 @@ assays such as Hi-C.")
 (define-public r-hitc
   (package
     (name "r-hitc")
-    (version "1.40.0")
+    (version "1.42.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "HiTC" version))
               (sha256
                (base32
-                "1pkshlrra26cad0hf8a54brlkazni6rsvrplh36azxapx5rpps4s"))))
+                "10m3pq22a8m8bbfkmq5r44ydg2668g6dxmxp7km47jxgf9hlqhcl"))))
     (properties `((upstream-name . "HiTC")))
     (build-system r-build-system)
     (propagated-inputs
@@ -14577,14 +16765,14 @@ provided.")
 (define-public r-hdf5array
   (package
     (name "r-hdf5array")
-    (version "1.24.1")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "HDF5Array" version))
        (sha256
         (base32
-         "1r1lg7k60qgb489xkypd4gvm1fmdlihvylb5va6xj58ipndbfday"))))
+         "1y25mlsqf2inij6w2825xxl30bdba971az6rjf7j9bnya3gpvi6h"))))
     (properties `((upstream-name . "HDF5Array")))
     (build-system r-build-system)
     (inputs
@@ -14608,14 +16796,14 @@ block processing.")
 (define-public r-rhdf5lib
   (package
     (name "r-rhdf5lib")
-    (version "1.18.2")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rhdf5lib" version))
        (sha256
         (base32
-         "1jpb8h7c724yz51zjfqs90bsqxgmy1rry2ra9qamsgqpr2j9764g"))
+         "0zxgpc2krfwqzm8c05cdlfs3dyyf5ll43ff9mw8xzj89wcmlcfx7"))
        (modules '((guix build utils)))
        (snippet
         '(begin
@@ -14688,14 +16876,14 @@ packages.")
 (define-public r-beachmat
   (package
     (name "r-beachmat")
-    (version "2.12.0")
+    (version "2.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "beachmat" version))
        (sha256
         (base32
-         "0fc6vvjjq1mfjfj2zqkap3rwvinnfqjs0cpk1447sspvd1rjya8c"))))
+         "0sa1wh997jfiz2y0dr7v12b7pvlf7icgv6arlyqy57winbnqa96m"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biocgenerics r-delayedarray r-matrix r-rcpp))
@@ -14714,13 +16902,13 @@ matrices.")
 (define-public r-cner
   (package
     (name "r-cner")
-    (version "1.32.0")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "CNEr" version))
        (sha256
-        (base32 "05zvr5fv8nprxqh2wvvrlf737dq242i20p1rpyqjaxihl6xl62kq"))))
+        (base32 "15y27ca14fdhn2prqgkyikff7p7490xn0bp2c7cnwhw173mm1syw"))))
     (properties `((upstream-name . "CNEr")))
     (build-system r-build-system)
     (inputs (list zlib))
@@ -14762,14 +16950,14 @@ advanced visualization of sets of conserved noncoding elements.")
 (define-public r-tfbstools
   (package
     (name "r-tfbstools")
-    (version "1.34.0")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "TFBSTools" version))
        (sha256
         (base32
-         "0l6j1r2cx7jfd39qzbyynk4jvzd81ys6yypzxjc97js4kkyrx29w"))))
+         "05kgkwmh5mcrm0xd81rzicysgknb8wrf71y2llikvma1b9c1g789"))))
     (properties `((upstream-name . "TFBSTools")))
     (build-system r-build-system)
     (propagated-inputs
@@ -14808,13 +16996,13 @@ provides a wrapper of de novo motif discovery software.")
 (define-public r-maftools
   (package
     (name "r-maftools")
-    (version "2.12.0")
+    (version "2.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "maftools" version))
        (sha256
-        (base32 "1gqfi95v4fs64n4walij0g2kds3fbbwp6lih5yakmgf6kj8fpkk6"))))
+        (base32 "1f1r0frikaj6aw137dk523gagkxdygg7gzc3pd303ds5cqynwiqx"))))
     (properties `((upstream-name . "maftools")))
     (build-system r-build-system)
     (propagated-inputs
@@ -14837,14 +17025,14 @@ customizable visualzations with minimal effort.")
 (define-public r-motifmatchr
   (package
     (name "r-motifmatchr")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "motifmatchr" version))
        (sha256
         (base32
-         "1ssn00mxwk23zr5na0vcmxvm69i68f0ga0wqlv1nk2isg0wpv878"))))
+         "01k2ngf4nj2cazb3a2c96by86xwdkdngzwhb73n2wadibamnqnfv"))))
     (properties `((upstream-name . "motifmatchr")))
     (build-system r-build-system)
     (propagated-inputs
@@ -14871,13 +17059,13 @@ This package wraps C++ code from the MOODS motif calling library.")
 (define-public r-chromvar
   (package
     (name "r-chromvar")
-    (version "1.18.0")
+    (version "1.20.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "chromVAR" version))
        (sha256
-        (base32 "0vhsvkm4kvln0002f13ayk57f9fmiz1kw9vwpsm1vds1vahd656m"))))
+        (base32 "1nhhpqhpvmw6b0nwxdwsjnakmfpxzpii8fmabwwg9bk8ni3zj5dq"))))
     (properties `((upstream-name . "chromVAR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -14918,14 +17106,14 @@ sequence (@code{DNAse-seq}) experiments.")
 (define-public r-singlecellexperiment
   (package
     (name "r-singlecellexperiment")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "SingleCellExperiment" version))
        (sha256
         (base32
-         "0s1aqbvlfnzijzfywjfpinqmxqj269dq2d3zlgf4xw9c1nwwnv7p"))))
+         "1y9c9wf3009w4qh03zpsmc0ff0nkzal673a4nql5c11cn55sza2g"))))
     (properties
      `((upstream-name . "SingleCellExperiment")))
     (build-system r-build-system)
@@ -14946,13 +17134,13 @@ libraries.")
 (define-public r-singler
   (package
     (name "r-singler")
-    (version "1.10.0")
+    (version "2.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "SingleR" version))
        (sha256
-        (base32 "0qbyc6ygw2xv3li9187i3axsw6ihwpa7pkvxvy9cagv7xck45c5y"))))
+        (base32 "05rw6l0d4n9m1dd7dp55zfripx036x1riwy83sx3aj5mw4r1awb6"))))
     (properties `((upstream-name . "SingleR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -14978,14 +17166,14 @@ cell types to infer the cell of origin of each single cell independently.")
 (define-public r-scuttle
   (package
     (name "r-scuttle")
-    (version "1.6.2")
+    (version "1.8.3")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scuttle" version))
        (sha256
         (base32
-         "0nnmq3wf436xaw4arc4y3ldvn6ilsg52xzbccmid0icb8z3y2kzn"))))
+         "1wgh28rj8m5dz89s9y4rzfy68d8ign6pcnnwj9g7h4sc3jfsg56i"))))
     (properties `((upstream-name . "scuttle")))
     (build-system r-build-system)
     (propagated-inputs
@@ -15013,13 +17201,13 @@ of other packages.")
 (define-public r-scater
   (package
     (name "r-scater")
-    (version "1.24.0")
+    (version "1.26.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "scater" version))
               (sha256
                (base32
-                "0dqirggw7my5nq4ln9q0ya18ciqplkz9gx318ffias9ag3yii5rw"))))
+                "1mjnf2y41lvni77g9hyw8qlvlsi5nxv5ha0fnch1kmw9814nycq3"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-beachmat
@@ -15032,8 +17220,10 @@ of other packages.")
            r-ggbeeswarm
            r-ggplot2
            r-ggrepel
+           r-ggrastr
            r-gridextra
            r-matrix
+           r-pheatmap
            r-rcolorbrewer
            r-rcppml
            r-rlang
@@ -15042,6 +17232,7 @@ of other packages.")
            r-scuttle
            r-singlecellexperiment
            r-summarizedexperiment
+           r-uwot
            r-viridis))
     (native-inputs
      (list r-knitr))
@@ -15055,14 +17246,14 @@ quality control.")
 (define-public r-scran
   (package
     (name "r-scran")
-    (version "1.24.0")
+    (version "1.26.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scran" version))
        (sha256
         (base32
-         "0xg7dl35915a65pmzkxdacsm4iqf97ayljdjljcvqx1ycmn7x68w"))))
+         "1sqc8pf1qzm24kf1l45da12wbzv0nxsy6l3v9fc8srmnvk37p04p"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-beachmat
@@ -15098,14 +17289,14 @@ variable and significantly correlated genes.")
 (define-public r-sparsematrixstats
   (package
     (name "r-sparsematrixstats")
-    (version "1.8.0")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "sparseMatrixStats" version))
        (sha256
         (base32
-         "0p12kay7p5zbfm2589wdx0n9jhgpf5fb2fsmkhn3p4ck4xcy13x2"))))
+         "1rq23ra4nnz9dx0gsg9bh8zcbz6s0pyvjwq30xl6g4hbqz927xb0"))))
     (properties
      `((upstream-name . "sparseMatrixStats")))
     (build-system r-build-system)
@@ -15123,14 +17314,14 @@ data in the column sparse format.")
 (define-public r-delayedmatrixstats
   (package
     (name "r-delayedmatrixstats")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DelayedMatrixStats" version))
        (sha256
         (base32
-         "1qlwv69c0r2w3zkmsr8r7w6sr3hf1ha0sfcrsjx4ks8f0ww7aqsv"))))
+         "0qcn7rlq0bsj11sc31wzks2xv900fpmbsblxp9cng5lj5cn2djk3"))))
     (properties
      `((upstream-name . "DelayedMatrixStats")))
     (build-system r-build-system)
@@ -15159,14 +17350,14 @@ memory usage and processing time is minimized.")
 (define-public r-mscoreutils
   (package
     (name "r-mscoreutils")
-    (version "1.8.0")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MsCoreUtils" version))
        (sha256
         (base32
-         "077x1zcy27x8akmagjn75j97082cgnahrbfw0qx08q455m5x3xzh"))))
+         "1shrvb2vmvk1m6xk59jqpvrxi8vzcr978aalbx1gjcmaqf6abzcq"))))
     (properties `((upstream-name . "MsCoreUtils")))
     (build-system r-build-system)
     (propagated-inputs
@@ -15188,13 +17379,13 @@ within the R for Mass Spectrometry packages.")
 (define-public r-msfeatures
   (package
     (name "r-msfeatures")
-    (version "1.4.0")
+    (version "1.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MsFeatures" version))
        (sha256
-        (base32 "111iqcq4q315pb4j8z427shin9b00p179m2s9h6dd7imvbd68yq3"))))
+        (base32 "1q1224w31wdaagfv8ysc1w0d0n34y547c0jzkff1vxri9pb0w1j1"))))
     (properties `((upstream-name . "MsFeatures")))
     (build-system r-build-system)
     (propagated-inputs
@@ -15218,14 +17409,14 @@ the respective packages (such as e.g. @code{xcms}).")
 (define-public r-biocio
   (package
     (name "r-biocio")
-    (version "1.6.0")
+    (version "1.8.0")
     (source
       (origin
         (method url-fetch)
         (uri (bioconductor-uri "BiocIO" version))
         (sha256
           (base32
-            "16j826w4zrmbgpmq6nyglcrjailsfv48ih1rz1qn383g7v503ydp"))))
+            "15d4xsn3k32q7lzcyxvs70f0jbh9fgwl3vi7xd6sqpggar12hh9f"))))
     (properties `((upstream-name . "BiocIO")))
     (build-system r-build-system)
     (propagated-inputs
@@ -15251,14 +17442,14 @@ as well as local access.  Developers can register a file extension, e.g.,
 (define-public r-msmseda
   (package
     (name "r-msmseda")
-    (version "1.34.0")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "msmsEDA" version))
        (sha256
         (base32
-         "0jnaq9ar4mnf3pfhka9hvk61p51ny9jws49xi8z29dq288b42b42"))))
+         "17xklsg483zd205q5hyxy6b3cgrb53pplb1wc7pmv5638y7nsq2v"))))
     (properties `((upstream-name . "msmsEDA")))
     (build-system r-build-system)
     (propagated-inputs
@@ -15274,14 +17465,14 @@ experiments, and visualize de influence of the involved factors.")
 (define-public r-msmstests
   (package
     (name "r-msmstests")
-    (version "1.34.0")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "msmsTests" version))
        (sha256
         (base32
-         "1wzdz0p9wmr243xkmymx9fwskafkyxgmlip4sd1fy2s06px7r0xi"))))
+         "10frsvqhi3i0v2w4q4q9xz1ykyf6s3nrjlmn94x3kd06p3s839k3"))))
     (properties `((upstream-name . "msmsTests")))
     (build-system r-build-system)
     (propagated-inputs
@@ -15303,14 +17494,14 @@ relevant, and the minimum expression of the most abundant condition.")
 (define-public r-catalyst
   (package
     (name "r-catalyst")
-    (version "1.20.1")
+    (version "1.22.0")
     (source
       (origin
         (method url-fetch)
         (uri (bioconductor-uri "CATALYST" version))
         (sha256
           (base32
-            "05vfqwa9qsm16px77s9bzygs6zymcxshymmpvz86a9l1cy1yxbza"))))
+            "0n3x5w074x5hhgdf2qa0pkma4vrjwrcgjna7hx0az6ixkgpbkrpv"))))
     (properties `((upstream-name . "CATALYST")))
     (build-system r-build-system)
     (propagated-inputs
@@ -15366,14 +17557,14 @@ preprocessing of cytometry data, including:
 (define-public r-erma
   (package
     (name "r-erma")
-    (version "1.12.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "erma" version))
        (sha256
         (base32
-         "1ilq01cr2ipxpmp422fikiz6nj4nasjhj0ikcagjn2zmmarpgi1b"))))
+         "06zxqzbzb0jrk357900gv1r2n81i49rbmrxla02f879kq2ik9cyd"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotationdbi
@@ -15406,14 +17597,14 @@ by Ernst and Kellis.")
 (define-public r-ggbio
   (package
     (name "r-ggbio")
-    (version "1.44.1")
+    (version "1.46.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ggbio" version))
        (sha256
         (base32
-         "0iyhjalwq1jmldpn20iv8l2kmz6sm20ddry2yz2zn7yq0wszp3vg"))))
+         "1gm3y1nx0ah8wcrg2dh1xd688izm2sijz7bhgsasxckmmkmkp60g"))))
     (build-system r-build-system)
     (arguments
      `(#:phases
@@ -15574,14 +17765,14 @@ family of feature/genome hypotheses.")
 (define-public r-gviz
   (package
     (name "r-gviz")
-    (version "1.40.1")
+    (version "1.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Gviz" version))
        (sha256
         (base32
-         "0as3sxhv21bqqrpvafcqim7798hhkzj3q40hy1rqyhv2lhj4rbvi"))))
+         "09j94kk3dd3bbfw6a2l14i7vd4rh11g9lxhw4zsm15vg71cm1lv9"))))
     (properties `((upstream-name . "Gviz")))
     (build-system r-build-system)
     (propagated-inputs
@@ -15623,14 +17814,14 @@ with your data.")
 (define-public r-gwascat
   (package
     (name "r-gwascat")
-    (version "2.28.1")
+    (version "2.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gwascat" version))
        (sha256
         (base32
-         "19ymdxj8966i4yk0zalfw23938cpv4q7pywg4qb242p44na5y9sl"))))
+         "0sj51cli1p8k7z1nl5rfswjlzrk9cqnpr1a1pr618gk74kfwqf5a"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotationdbi
@@ -15657,13 +17848,13 @@ EMBL-EBI GWAS catalog.")
 (define-public r-kegggraph
   (package
     (name "r-kegggraph")
-    (version "1.56.0")
+    (version "1.58.3")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "KEGGgraph" version))
        (sha256
-        (base32 "15pq040pcg8hr18xixmjp59xb7mgvygjv6kisqk8yv99l1611ndx"))))
+        (base32 "1s5j7zdp8ck4vhca81i4b6qclhwi56gmz8brawrxj3szvwmxf3y6"))))
     (properties `((upstream-name . "KEGGgraph")))
     (build-system r-build-system)
     (propagated-inputs
@@ -15681,14 +17872,14 @@ functionalities including parsing, graph operation, visualization and etc.")
 (define-public r-ldblock
   (package
     (name "r-ldblock")
-    (version "1.26.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ldblock" version))
        (sha256
         (base32
-         "08ss03b93czwb4x60hsi30ad4lmamvq5mxa8nj0g18z68qcraijm"))))
+         "0i8v4wfp207f5dpf3y2n8fqn7mc4khj92gb209vzc3y3kbwp2c6n"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biocgenerics
@@ -15805,13 +17996,13 @@ other functional sequencing data.")
 (define-public r-pathview
   (package
     (name "r-pathview")
-    (version "1.36.0")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "pathview" version))
        (sha256
-        (base32 "1472k107f21cflbx2fip92g8gl9wlwxgwfvgvl73ma0y0jzs0qdq"))))
+        (base32 "0p7cdq03863zpw009prs1yh3gps1kw135anjfq6wpdkwza7xy4py"))))
     (properties `((upstream-name . "pathview")))
     (build-system r-build-system)
     (propagated-inputs
@@ -15839,14 +18030,14 @@ large-scale and fully automated analysis.")
 (define-public r-snpstats
   (package
     (name "r-snpstats")
-    (version "1.46.0")
+    (version "1.48.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "snpStats" version))
        (sha256
         (base32
-         "0a5b5nqc7n965jk45ijwkzbn416ib4gfhp8xl39z8f2bdskip4a2"))))
+         "14rkrav4iydc85194skdy33sk365pjmmvxxvzaxxh0k9ds009qwx"))))
     (properties `((upstream-name . "snpStats")))
     (build-system r-build-system)
     (inputs (list zlib))
@@ -15863,14 +18054,14 @@ the earlier snpMatrix package, allowing for uncertainty in genotypes.")
 (define-public r-chromstar
   (package
     (name "r-chromstar")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "chromstaR" version))
        (sha256
         (base32
-         "1xjwmnr4hk8v3nwvhqd6ixk5qr2dv0n4mb9wd6nl7cgjfhjsdgj7"))))
+         "17p22vsmb9h8ap0f2rzyg2r71srj3sxiapzyaz1csad2vfjxfi2r"))))
     (properties `((upstream-name . "chromstaR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -15901,14 +18092,14 @@ analyses.")
 (define-public r-guitar
   (package
     (name "r-guitar")
-    (version "2.12.0")
+    (version "2.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Guitar" version))
        (sha256
         (base32
-         "09grsasnnk7rmlzjh4lhas9r5spzcsrvmdqj6fx1dk22sckcqahh"))))
+         "0lrw1v82amr54bkfh98953b16fhlgd1i6kz1g7zy8gj0hd417ms1"))))
     (properties `((upstream-name . "Guitar")))
     (build-system r-build-system)
     (propagated-inputs
@@ -15954,14 +18145,14 @@ visualizations for publication-quality multi-panel figures.")
 (define-public r-ballgown
   (package
     (name "r-ballgown")
-    (version "2.28.0")
+    (version "2.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ballgown" version))
        (sha256
         (base32
-         "0l8q3fymskxmsi5jcikzjz5xi66lpzgv7bjymir4izah2v68z708"))))
+         "0iy24vj4lg1k4fzdxf9blc47xsp4dmplajgabsb2s925l7jpxfvw"))))
     (properties `((upstream-name . "ballgown")))
     (build-system r-build-system)
     (propagated-inputs
@@ -15988,14 +18179,14 @@ to annotation.")
 (define-public r-megadepth
   (package
     (name "r-megadepth")
-    (version "1.6.0")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "megadepth" version))
        (sha256
         (base32
-         "0qq82dmd3drr2bhn51bgbc6ml40klfmmhj6wdj72n9ya6n60lwy8"))))
+         "1krk5iqqzkkkxfgsvi9j6mj14i2rzisrrq0xmxjsrkgfh19awhr8"))))
     (properties `((upstream-name . "megadepth")))
     (build-system r-build-system)
     (inputs (list megadepth))
@@ -16021,14 +18212,14 @@ regions or annotations of your choice from BigWig files.")
 (define-public r-beclear
   (package
     (name "r-beclear")
-    (version "2.12.0")
+    (version "2.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BEclear" version))
        (sha256
         (base32
-         "0x43yfnmb2d782g3g52nqdfs90i3zrrlqz8qy3ybmgv5f8n92p15"))))
+         "05znaj2fialxi937mhj2dlrm3v4j2wgqafcy78qrkz7xxn13pr01"))))
     (properties `((upstream-name . "BEclear")))
     (build-system r-build-system)
     (propagated-inputs
@@ -16037,6 +18228,7 @@ regions or annotations of your choice from BigWig files.")
            r-data-table
            r-dixontest
            r-futile-logger
+           r-ids
            r-matrix
            r-rcpp
            r-rdpack))
@@ -16054,14 +18246,14 @@ real numbers.")
 (define-public r-bgeecall
   (package
     (name "r-bgeecall")
-    (version "1.12.1")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BgeeCall" version))
        (sha256
         (base32
-         "1g12cms66zb45p347h3b358vjhnq76galvwqwq86xby4hnwpdzkh"))))
+         "05w6b10vc4mmwdqnkcj7vnfigk03f03n776vqhlb38k0lx8k4hk3"))))
     (properties `((upstream-name . "BgeeCall")))
     (build-system r-build-system)
     (propagated-inputs
@@ -16090,14 +18282,14 @@ all RNA-Seq libraries of each species integrated in Bgee.")
 (define-public r-bgeedb
   (package
     (name "r-bgeedb")
-    (version "2.22.3")
+    (version "2.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BgeeDB" version))
        (sha256
         (base32
-         "1f6lrazaibbz21sqvj59rq6ps9m1riw2y0kyidbn29mxf4ibwh3k"))))
+         "14fja1dikzq60zjx1arcv1q16qd0hmibqjy0nbaivmk3zh16spkc"))))
     (properties `((upstream-name . "BgeeDB")))
     (build-system r-build-system)
     (propagated-inputs
@@ -16124,14 +18316,14 @@ anatomical terms, mapped to genes by expression patterns.")
 (define-public r-biobtreer
   (package
     (name "r-biobtreer")
-    (version "1.8.0")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biobtreeR" version))
        (sha256
         (base32
-         "0cx46hdqqm6mbj0vp4y86axv0qccd4sgk2jwwjvnqp5pynq9bbqa"))))
+         "1j6w19k124x46gj2p8f1z0i2c03yhiiy1w0fqf504b2r7wy90jxc"))))
     (properties `((upstream-name . "biobtreeR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -16148,14 +18340,14 @@ mappings functionalities.")
 (define-public r-minet
   (package
     (name "r-minet")
-    (version "3.54.0")
+    (version "3.56.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "minet" version))
        (sha256
         (base32
-         "0q6jw2jqkl9qynjpzaygz45c7dmx1l5y2d8s1illpcf87siawcam"))))
+         "1xknyc2m03dyqrnx6np2y2lr41w06arl114f6cncl6wsnanqxzrz"))))
     (properties `((upstream-name . "minet")))
     (build-system r-build-system)
     (propagated-inputs
@@ -16170,14 +18362,14 @@ information networks from data.")
 (define-public r-genetclassifier
   (package
     (name "r-genetclassifier")
-    (version "1.36.0")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "geNetClassifier" version))
        (sha256
         (base32
-         "1kh7mp5h0n7yd1klcd7w4v7i3fh9pkmvgf7189wangfzbcsr4f70"))))
+         "1ahlml1ssjmg126ki1phdprq4v0nawzbbfq8jray5ypaj32qx3r2"))))
     (properties
      `((upstream-name . "geNetClassifier")))
     (build-system r-build-system)
@@ -16195,14 +18387,14 @@ interface to query the classifier.")
 (define-public r-dir-expiry
   (package
     (name "r-dir-expiry")
-    (version "1.4.0")
+    (version "1.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "dir.expiry" version))
        (sha256
         (base32
-         "098wzm8hlpy70c99k2sl4k8z2dllhw7rwdj8dhcskr7kaw71k3sq"))))
+         "1ix31jcfi3dg12pa0sz4k4izwc9rsydy6krl7f949lkam2g7s5f8"))))
     (properties `((upstream-name . "dir.expiry")))
     (build-system r-build-system)
     (propagated-inputs (list r-filelock))
@@ -16219,14 +18411,14 @@ eliminating obsolete caches generated by old versions of packages.")
 (define-public r-basilisk-utils
   (package
     (name "r-basilisk-utils")
-    (version "1.8.0")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "basilisk.utils" version))
        (sha256
         (base32
-         "1jnqv0rlljkq27rd4ixl763v335f2aanm4fzr386yc81fj4vnmhk"))))
+         "0gh29w8arg0glawprwshaixv07y756c4lx21h8jjbqlsrbspp8fw"))))
     (properties
      `((upstream-name . "basilisk.utils")))
     (build-system r-build-system)
@@ -16243,14 +18435,14 @@ package, primarily for creation of the underlying Conda instance.")
 (define-public r-basilisk
   (package
     (name "r-basilisk")
-    (version "1.8.0")
+    (version "1.10.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "basilisk" version))
        (sha256
         (base32
-         "1p90wq8a9wrpqpgmcy4zgh5skdw65gg2gsb3lnx78zk9khq0yyzh"))))
+         "14sgm3ia7jj5jckysqkljrffafg6rl8i7fgzsxv8ycnrwbd05d09"))))
     (properties `((upstream-name . "basilisk")))
     (build-system r-build-system)
     (propagated-inputs
@@ -16269,14 +18461,14 @@ Python environments in a single R session.")
 (define-public r-biocthis
   (package
     (name "r-biocthis")
-    (version "1.6.0")
+    (version "1.8.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biocthis" version))
        (sha256
         (base32
-         "1hdgjp00d2si3mr7m1d289i9wn7g927z6n8n27d5sm94lb91qln0"))))
+         "0zmiaixknwxv72l4fygrn0qr3mvl7kqfbqgflnavs0wxx6xdjqgn"))))
     (properties `((upstream-name . "biocthis")))
     (build-system r-build-system)
     (arguments
@@ -16303,14 +18495,14 @@ Bioconductor-friendly.")
 (define-public r-biocdockermanager
   (package
     (name "r-biocdockermanager")
-    (version "1.8.0")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocDockerManager" version))
        (sha256
         (base32
-         "0kl6r8ad728a8dvqx0safj7v5gj1rxxcdiw44jkr1pd5ddv0xbi6"))))
+         "13l5shmiiv4wl9m5xnwzagjxqrchjg9znvcgf7hv8f263l2yc8qm"))))
     (properties
      `((upstream-name . "BiocDockerManager")))
     (build-system r-build-system)
@@ -16333,14 +18525,14 @@ the Bioconductor project.")
 (define-public r-biodb
   (package
     (name "r-biodb")
-    (version "1.4.0")
+    (version "1.6.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biodb" version))
        (sha256
         (base32
-         "02i0n29bp9d9p1ibslxca5m37qsgny2hlgg7d364lf7kc6y2bqni"))))
+         "0mbqsias2ajw29d1wgl10y2cjqv3slrsgifccz0kh9l5r6bk28vz"))))
     (properties `((upstream-name . "biodb")))
     (build-system r-build-system)
     (propagated-inputs
@@ -16378,14 +18570,14 @@ separate published packages.")
 (define-public r-biomformat
   (package
     (name "r-biomformat")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biomformat" version))
        (sha256
         (base32
-         "12wqjipxhngmlnrdmx329dqmkmy2wa4nkkrhwaqv2nwy90dncs9n"))))
+         "0728fpj05bvna5lpm29pdbn4slfmq16nz35as086ddbl2hhc9ni1"))))
     (properties `((upstream-name . "biomformat")))
     (build-system r-build-system)
     (propagated-inputs
@@ -16407,14 +18599,14 @@ as extensions of common core functions/methods.")
 (define-public r-mvcclass
   (package
     (name "r-mvcclass")
-    (version "1.70.0")
+    (version "1.72.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MVCClass" version))
        (sha256
         (base32
-         "0apcjlq4i2mg8mlfqgvlcsqkiy51whzid3nd0m830jff0ywgh47g"))))
+         "1yzb7m7vk50f9x1g8yb95wlmpccj3n4qgczz46lvhsk7hkifybzq"))))
     (properties `((upstream-name . "MVCClass")))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/MVCClass")
@@ -16427,14 +18619,14 @@ design.")
 (define-public r-biomvcclass
   (package
     (name "r-biomvcclass")
-    (version "1.64.0")
+    (version "1.66.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BioMVCClass" version))
        (sha256
         (base32
-         "078pnyygbvbfxziqspfr1nn78w67xyb4qmiwc34czga5psblvfwz"))))
+         "1xclmwxps7yvqnaw8kn6z4mlpx6v8xfzyly4cadsjaj2qm535xxk"))))
     (properties `((upstream-name . "BioMVCClass")))
     (build-system r-build-system)
     (propagated-inputs
@@ -16449,14 +18641,14 @@ design.")
 (define-public r-biomvrcns
   (package
     (name "r-biomvrcns")
-    (version "1.36.0")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biomvRCNS" version))
        (sha256
         (base32
-         "0i576g7pkivqaxff1pkb760mdpx8v9fh071aic1mwfnlfa7k87ln"))))
+         "0n026b744ah5kcnipsyiqqs7vlz5n5im1kgv35i2pgxyzvf7a8sn"))))
     (properties `((upstream-name . "biomvRCNS")))
     (build-system r-build-system)
     (propagated-inputs
@@ -16474,32 +18666,32 @@ using aCGH or sequencing.")
 (define-public r-bionero
   (package
     (name "r-bionero")
-    (version "1.4.0")
+    (version "1.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BioNERO" version))
        (sha256
         (base32
-         "1nyzjbl0gcwvbj2nxfwykirikf8j3rsx5ny45bqjbcb4r23k65kj"))))
+         "10nwgp8a9chn33p5k7cdp920rraiw187xfrylyd9bq010c7vp7xh"))))
     (properties `((upstream-name . "BioNERO")))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biocparallel
            r-complexheatmap
-           r-deseq2
            r-dynamictreecut
            r-genie3
            r-ggnetwork
            r-ggnewscale
            r-ggplot2
-           r-ggpubr
+           r-ggrepel
            r-igraph
            r-intergraph
            r-matrixstats
            r-minet
            r-netrep
            r-networkd3
+           r-patchwork
            r-rcolorbrewer
            r-reshape2
            r-summarizedexperiment
@@ -16530,14 +18722,14 @@ networks.")
 (define-public r-bionet
   (package
     (name "r-bionet")
-    (version "1.56.0")
+    (version "1.58.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BioNet" version))
        (sha256
         (base32
-         "0kcw71j4nmdkn373wk21ak6h0v4gycivnfrklb72kk1qcmsy1wrm"))))
+         "12c6m7dzwkdh4bk1c5xmzm5ajrsba7v62mag1f3rrpmrapdh6s0j"))))
     (properties `((upstream-name . "BioNet")))
     (build-system r-build-system)
     (propagated-inputs
@@ -16559,14 +18751,14 @@ scoring subnetwork.")
 (define-public r-bionetstat
   (package
     (name "r-bionetstat")
-    (version "1.16.1")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BioNetStat" version))
        (sha256
         (base32
-         "0zs6pymvxb95sji0rnnzaz3whj7hsvj2kl4n4gzj7w1q0prbfpb2"))))
+         "1h99d6gnqw5v9ha2169zfhw9cvxhyjgkf4zm8qj1i03h2cywapgv"))))
     (properties `((upstream-name . "BioNetStat")))
     (build-system r-build-system)
     (propagated-inputs
@@ -16601,14 +18793,14 @@ network and metabolic pathways view.")
 (define-public r-bioqc
   (package
     (name "r-bioqc")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BioQC" version))
        (sha256
         (base32
-         "0vb2nnzqvyv25pw8qshcmijravswafg0858pkgqjgiv7wsr2mn3m"))))
+         "1ssxsxdm8vmlrmvvdz5p98apd3xsal1h3ss8556g83kgw830zsxf"))))
     (properties `((upstream-name . "BioQC")))
     (build-system r-build-system)
     (propagated-inputs
@@ -16627,14 +18819,14 @@ optimised for high performance.")
 (define-public r-biotip
   (package
     (name "r-biotip")
-    (version "1.10.0")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BioTIP" version))
        (sha256
         (base32
-         "1sihi5zy7mlabh3ix1wvdqz8ibfq1avl8bnxjhvxyzq40zbcklh6"))))
+         "1n90n4vz0cwz8irwpmrkm9qcyvk5rssl2v6wrzny4zwhzjkmvlni"))))
     (properties `((upstream-name . "BioTIP")))
     (build-system r-build-system)
     (propagated-inputs
@@ -16657,14 +18849,14 @@ help unravel disease regulatory trajectory.")
 (define-public r-biotmle
   (package
     (name "r-biotmle")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biotmle" version))
        (sha256
         (base32
-         "1frig90krvfdk6nwpmslpj0pvligyzwzfwwci7hzwcmbglk5jj22"))))
+         "1sbwbz0xdws31lsh46mfcijqmi6rm050r1d6vwii65q686x5j43w"))))
     (properties `((upstream-name . "biotmle")))
     (build-system r-build-system)
     (propagated-inputs
@@ -16699,14 +18891,14 @@ ensemble machine learning for the estimation of nuisance functions.")
 (define-public r-bsseq
   (package
     (name "r-bsseq")
-    (version "1.32.0")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bsseq" version))
        (sha256
         (base32
-         "1jpfib2vb6hd7pgh3d33jgch24lba175zmbalwsbgvlmmyyf1ki5"))))
+         "0rd0ihr1ai1kvly2zf5y2qx3qyhk3ag2mdsrwqnzs67xkv99glsf"))))
     (properties `((upstream-name . "bsseq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -16742,17 +18934,54 @@ ensemble machine learning for the estimation of nuisance functions.")
 visualizing bisulfite sequencing data.")
     (license license:artistic2.0)))
 
+(define-public r-dada2
+  (package
+    (name "r-dada2")
+    (version "1.26.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "dada2" version))
+              (sha256
+               (base32
+                "1cdfq4qa4kkfkqnkyxyr109hbvj5li396rm3p2b11qm2pxmfd7kc"))))
+    (properties `((upstream-name . "dada2")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biocgenerics
+           r-biostrings
+           r-ggplot2
+           r-iranges
+           r-rcpp
+           r-rcppparallel
+           r-reshape2
+           r-shortread
+           r-xvector))
+    (native-inputs (list r-knitr))
+    (home-page "https://benjjneb.github.io/dada2/")
+    (synopsis
+     "Accurate, high-resolution sample inference from amplicon sequencing data")
+    (description
+     "The dada2 package infers exact @dfn{amplicon sequence variants} (ASVs)
+from high-throughput amplicon sequencing data, replacing the coarser and less
+accurate OTU clustering approach.  The dada2 pipeline takes as input
+demultiplexed fastq files, and outputs the sequence variants and their
+sample-wise abundances after removing substitution and chimera errors.
+Taxonomic classification is available via a native implementation of the RDP
+naive Bayesian classifier, and species-level assignment to 16S rRNA gene
+fragments by exact matching.")
+    (license license:lgpl2.0)))
+
 (define-public r-dmrseq
   (package
     (name "r-dmrseq")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "dmrseq" version))
        (sha256
         (base32
-         "1c99l62fi26bnbvpzrlsvvs722za0l5vfhddcrhzzzasabhccb4n"))))
+         "1zx62lbj0am85p0c1vk06s7qf8294vk8yyh67nkiqc7xgqqwybyk"))))
     (properties `((upstream-name . "dmrseq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -16791,13 +19020,13 @@ interest on transformed methylation proportions.")
 (define-public r-omicade4
   (package
     (name "r-omicade4")
-    (version "1.36.0")
+    (version "1.38.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "omicade4" version))
               (sha256
                (base32
-                "1l7w3sczsimg640klq8navgdcwjj090wjqd40n4mw76pny2xj2lj"))))
+                "1w9fsg0r6ir9nmmpf08b1mh8mnrzxk3f398y1w5dg34fdz4phgpg"))))
     (properties `((upstream-name . "omicade4")))
     (build-system r-build-system)
     (propagated-inputs (list r-ade4 r-biobase r-made4))
@@ -16810,13 +19039,13 @@ interest on transformed methylation proportions.")
 (define-public r-omnipathr
   (package
     (name "r-omnipathr")
-    (version "3.4.0")
+    (version "3.5.25")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "OmnipathR" version))
        (sha256
-        (base32 "0vk0fv09j3ql78mzzhdxwxb2b83qqdz2qfd8wpp1vydmcx2vvgni"))))
+        (base32 "1a0d4vf8i45h1fifswx9lhk6fk0z8sxfnav35psz9kvmxxab9698"))))
     (properties `((upstream-name . "OmnipathR")))
     (build-system r-build-system)
     (arguments
@@ -16836,12 +19065,14 @@ interest on transformed methylation proportions.")
            r-later
            r-logger
            r-magrittr
+           r-rmarkdown
            r-progress
            r-purrr
            r-rappdirs
            r-readr
            r-readxl
            r-rlang
+           r-rvest
            r-stringr
            r-tibble
            r-tidyr
@@ -16863,14 +19094,14 @@ for ligand activity prediction from transcriptomics data.")
 (define-public r-biscuiteer
   (package
     (name "r-biscuiteer")
-    (version "1.10.0")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biscuiteer" version))
        (sha256
         (base32
-         "0y7vbdaafiga16yr0d22w1v4p0jmczndcar0r0km06f5y1b74amr"))))
+         "1fq2nj0vclpxavqj5qx7jc3ympg00izxn9fpy4mlhyp9l921z13m"))))
     (properties `((upstream-name . "biscuiteer")))
     (build-system r-build-system)
     (propagated-inputs
@@ -16915,13 +19146,13 @@ estimates, etc.")
 (define-public r-tcgabiolinks
   (package
     (name "r-tcgabiolinks")
-    (version "2.24.3")
+    (version "2.25.3")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "TCGAbiolinks" version))
        (sha256
-        (base32 "0visvfhzaf0p1rb5vjkmw1c91zfxpks8nl9nbl9xlnpm8lkmmkms"))))
+        (base32 "0daq7093yipry8pp6fj6pj8x1njxs8j6cz7875qkfmzqkbis4vql"))))
     (properties `((upstream-name . "TCGAbiolinks")))
     (build-system r-build-system)
     (propagated-inputs
@@ -16970,13 +19201,13 @@ starburst plots) in order to easily develop complete analysis pipelines.")
 (define-public r-tricycle
   (package
     (name "r-tricycle")
-    (version "1.4.0")
+    (version "1.6.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "tricycle" version))
               (sha256
                (base32
-                "0bjkajcz6xcfak6071d0ihakrvgf7s0pmkn6vqkjd6yxbfld7zln"))))
+                "0b5agqhywg23zxf0f9s1vfbzs7s7ijf9c716s7hwjprxfdz5znvw"))))
     (properties `((upstream-name . "tricycle")))
     (build-system r-build-system)
     (propagated-inputs
@@ -17009,14 +19240,14 @@ embeddings and functions to build new reference.")
 (define-public r-tximeta
   (package
     (name "r-tximeta")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "tximeta" version))
        (sha256
         (base32
-         "1vq7x1sf5h8iwdalalbrybxzbq47s2ymb75himj5wkv77mgcivfl"))))
+         "0v1s5ssinyrizpg2i88dn2ckzs4i16hjfg2pzxhal3ypsiw24qna"))))
     (properties `((upstream-name . "tximeta")))
     (build-system r-build-system)
     (propagated-inputs
@@ -17050,13 +19281,13 @@ reproducibility.")
 (define-public r-phyloseq
   (package
     (name "r-phyloseq")
-    (version "1.40.0")
+    (version "1.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "phyloseq" version))
        (sha256
-        (base32 "0hcyv4ziyaw74mc9vf7bad3q9izi9p0whg3hspbs6w8b3hp34y2k"))))
+        (base32 "07zi059v6zwrm31qwc7fmg35fwqlqfb6c30wwj9q4m2y67srnskk"))))
     (properties `((upstream-name . "phyloseq")))
     (build-system r-build-system)
     (propagated-inputs