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

1 files changed, 480 insertions, 4 deletions

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d684e4249b..f157523a76 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -719,6 +719,40 @@ suite native in R.")
 for all types of microbial diversity analyses.")
       (license license:expat))))
 
+(define-public r-codeandroll2
+  (let ((commit "d58e258851a5c0b430e8620d34dbeefb597c548f")
+        (revision "1"))
+    (package
+      (name "r-codeandroll2")
+      (version (git-version "2.3.6" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/vertesy/CodeAndRoll2")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "0sy88mfgw6qqhpnlc5020qzr1jllkcrxfhl2lw42bkl5nb56is71"))))
+      (properties `((upstream-name . "CodeAndRoll2")))
+      (build-system r-build-system)
+      (propagated-inputs (list r-colorramps
+                               r-dplyr
+                               r-gplots
+                               r-gtools
+                               r-plyr
+                               r-rcolorbrewer
+                               r-sessioninfo
+                               r-sm
+                               r-stringendo
+                               r-stringr))
+      (home-page "https://github.com/vertesy/CodeAndRoll2")
+      (synopsis "CodeAndRoll2 for vector, matrix and list manipulations")
+      (description
+       "CodeAndRoll2 is a set of more than 130 productivity functions.
+These functions are used by MarkdownReports, ggExpress, and SeuratUtils.")
+      (license license:gpl3))))
+
 (define-public r-conospanel
   (let ((commit "39e76b201a783b4e92fd615010a735a61746fbb9")
         (revision "1"))
@@ -743,6 +777,47 @@ each with 3000 cells.  There are two samples which are bone marrow (BM), and
 two samples which are cord blood (CB).")
       (license license:gpl3))))
 
+(define-public r-conqur
+  (let ((commit "c7a88794efd4ecfe4d96988dceeec3b410222e48")
+        (revision "1"))
+    (package
+      (name "r-conqur")
+      (version (git-version "2.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/wdl2459/ConQuR")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "19a7p2l67mgjy99i5ksjxlhzaqmrnyi1vzvwnhgnx2jrr6crj7rq"))))
+      (properties `((upstream-name . "ConQuR")))
+      (build-system r-build-system)
+      (propagated-inputs (list r-ade4
+                               r-ape
+                               r-compositions
+                               r-cqrreg
+                               r-doparallel
+                               r-dplyr
+                               r-fastdummies
+                               r-glmnet
+                               r-gplots
+                               r-gunifrac
+                               r-quantreg
+                               r-randomforest
+                               r-rocr
+                               r-vegan))
+      (native-inputs (list r-knitr))
+      (home-page "https://github.com/wdl2459/ConQuR")
+      (synopsis "Batch effects removal for microbiome data")
+      (description
+       "This package conducts batch effects removal from a taxa read count
+table by a conditional quantile regression method.  The distributional
+attributes of microbiome data - zero-inflation and over-dispersion, are
+simultaneously considered.")
+      (license license:gpl3))))
+
 (define-public r-p2data
   (let ((commit "7d4c0e17d7899f9d9b08ab2bf455abe150912f4c")
         (revision "1"))
@@ -793,6 +868,57 @@ high-throughput sequence analysis.  The package is primarily useful to
 developers of other R packages who wish to make use of HTSlib.")
       (license license:lgpl2.0+))))
 
+(define-public r-stringendo
+  (let ((commit "83b8f2d82a09b33b9e895438bb523a021138be01")
+        (revision "1"))
+    (package
+      (name "r-stringendo")
+      (version (git-version "0.3.4" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/vertesy/Stringendo")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "1ap0nhbyd6xx0yl2vgmwk38p22yrkv4k9hw13r35z4wf343rry6v"))))
+      (properties `((upstream-name . "Stringendo")))
+      (build-system r-build-system)
+      (propagated-inputs (list r-devtools r-usethis))
+      (home-page "https://github.com/vertesy/Stringendo")
+      (synopsis "Stringendo is a string parsing library")
+      (description
+       "This package provides string parsing functionalites for generating
+plotnames, filenames and paths.")
+      (license license:gpl3))))
+
+(define-public r-readwriter
+  (let ((commit "71454f4aa706f5d2fbe606acd95abc14224e7058")
+        (revision "1"))
+    (package
+      (name "r-readwriter")
+      (version (git-version "0.2.9" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/vertesy/ReadWriter")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "0sp27smhdva2hi2x0svia2l56k8xrh7p5akn78g5b0lcvz4x3hd7"))))
+      (properties `((upstream-name . "ReadWriter")))
+      (build-system r-build-system)
+      (propagated-inputs
+       (list r-gdata r-gtools r-openxlsx r-readr r-stringendo))
+      (home-page "https://github.com/vertesy/ReadWriter")
+      (synopsis "Functions to read and write files conveniently")
+      (description
+       "ReadWriter is a set of R functions to read and write files
+conveniently.")
+      (license license:gpl3))))
+
 (define-public r-streamgraph
   (let ((commit "76f7173ec89d456ace5943a512e20b1f6810bbcb")
         (revision "1"))
@@ -1262,8 +1388,7 @@ demultiplexing step.")
      (list python-black
            python-flake8
            python-poetry-core
-           python-pytest
-           python-pre-commit))
+           python-pytest))
     (home-page "https://github.com/JonathanShor/DoubletDetection")
     (synopsis
      "This is a package to detect doublets in single-cell RNA-seq count matrices")
@@ -3846,6 +3971,80 @@ sequencing data.  It uses paired-ends and split-reads to sensitively and
 accurately delineate genomic rearrangements throughout the genome.")
     (license license:gpl3+)))
 
+(define-public transanno
+  (package
+    (name "transanno")
+    (version "0.3.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/informationsea/transanno")
+             ;; Corresponds to tag v0.3.0
+             (commit "df49050c92644ea12d9d5c6fae2186ca436dbca3")))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "1jpn7s3cnd9ybk4lmfbhj2arhf6cmrv7jp74n7n87m3a3irkaif1"))
+       (snippet
+        '(with-output-to-file "liftover-rs/build.rs"
+           (lambda _
+             (format #true
+                     "fn main() {~@
+                        println!(\"cargo:rustc-link-lib=lzma\");~@
+                        }~%"))))))
+    (build-system cargo-build-system)
+    (arguments
+     (list
+      #:install-source? #false          ;fails
+      #:tests? #false                   ;"cargo test" ignores build.rs
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'prepare-test-files
+            (lambda _
+              (delete-file "Cargo.lock")
+              (substitute* "liftover-rs/Cargo.toml"
+                (("anyhow = \"1\"") "anyhow = \"1.0.65\""))
+              (substitute* "liftover-rs/prepare-test.sh"
+                (("/bin/bash")
+                 (string-append #$(this-package-native-input "bash")
+                                "/bin/bash")))
+              (invoke "bash" "prepare-test-files.sh")))
+          (add-before 'patch-cargo-checksums 'do-not-build-xz
+            (lambda _
+              ;; Detection of liblzma (in rust-lzma-sys, pulled in by
+              ;; rust-hts-sys) doesn't seem to work, or perhaps it really does
+              ;; request a static build somewhere.
+              (substitute* "guix-vendor/rust-lzma-sys-0.1.17.tar.xz/build.rs"
+                (("if .want_static && .msvc && pkg_config::probe_library\\(\"liblzma\"\\).is_ok\\(\\)") ""))))
+          (add-before 'install 'chdir
+            (lambda _ (chdir "transanno"))))
+      #:cargo-inputs
+      `(("rust-anyhow" ,rust-anyhow-1)
+        ("rust-autocompress" ,rust-autocompress-0.2)
+        ("rust-bio" ,rust-bio-0.41)
+        ("rust-clap" ,rust-clap-2)
+        ("rust-csv" ,rust-csv-1)
+        ("rust-flate2" ,rust-flate2-1)
+        ("rust-indexmap" ,rust-indexmap-1)
+        ("rust-log" ,rust-log-0.4)
+        ("rust-nom" ,rust-nom-5)
+        ("rust-once-cell" ,rust-once-cell-1)
+        ("rust-pretty-env-logger" ,rust-pretty-env-logger-0.3)
+        ("rust-regex" ,rust-regex-1)
+        ("rust-thiserror" ,rust-thiserror-1)
+        ("rust-serde" ,rust-serde-1)
+        ("rust-serde-json" ,rust-serde-json-1))
+      #:cargo-development-inputs
+      `(("rust-clap" ,rust-clap-2)
+        ("rust-lazy-static" ,rust-lazy-static-1))))
+    (native-inputs (list bash))
+    (home-page "https://github.com/informationsea/transanno")
+    (synopsis "LiftOver tool for new genome assemblies")
+    (description "This package provides an accurate VCF/GFF3/GTF LiftOver tool
+for new genome assemblies.")
+    (license license:gpl3+)))
+
 (define-public trf
   (package
     (name "trf")
@@ -8219,6 +8418,43 @@ sequence.")
     (supported-systems '("i686-linux" "x86_64-linux"))
     (license license:bsd-3)))
 
+(define-public r-ggexpress
+  (let ((commit "82f169385f87af328ff971195c2f64ff3c573a8a")
+        (revision "1"))
+    (package
+      (name "r-ggexpress")
+      (version (git-version "0.6.6" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/vertesy/ggExpress")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "122hnw8xv33ngcd4fd7hmf817a06ih1knrxxi0cgklj1fwinm0z4"))))
+      (properties `((upstream-name . "ggExpress")))
+      (build-system r-build-system)
+      (propagated-inputs (list r-cowplot
+                               r-ggplot2
+                               r-ggpubr
+                               r-markdownhelpers
+                               r-markdownreports
+                               r-rcolorbrewer
+                               r-sessioninfo
+                               r-seurat
+                               r-sm
+                               r-stringendo
+                               r-tidyverse))
+      (home-page "https://github.com/vertesy/ggExpress")
+      (synopsis
+       "This is a fast tool to create, annotate and export plots in R")
+      (description
+       "This package is a set of R functions for generating precise figures.
+This tool helps you to create clean markdown reports about what you just
+discovered with your analysis script.")
+      (license license:gpl3))))
+
 (define-public r-gg3d
   (let ((commit "ffdd837d30c1671cd0895db94bdd7b1594dbfcb0")
         (revision "1"))
@@ -8535,7 +8771,10 @@ Pore-C concatemers.")
                                r-seurat
                                r-singlecellexperiment
                                r-slingshot
-                               r-summarizedexperiment))
+                               r-summarizedexperiment
+                               python
+                               python-scrublet
+                               python-doubletdetection))
       (home-page "https://github.com/xnnba1984/DoubletCollection")
       (synopsis "Tool for finding doublets in scRNA-seq data")
       (description
@@ -8544,6 +8783,46 @@ doublet-detection methods.  In addition, this tool is used for execution and
 benchmark of those eight mentioned methods.")
       (license license:gpl3+))))
 
+(define-public r-plsdabatch
+  (let ((commit "4aadf3a99709afae462db310386b6cf5db20088c")
+        (revision "1"))
+    (package
+      (name "r-plsdabatch")
+      (version (git-version "0.2.3" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/EvaYiwenWang/PLSDAbatch")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "047l923lq2ji7rwybh9b9zkblzvvhkpli5gb2x8g2q9f2n5022nr"))))
+      (properties `((upstream-name . "PLSDAbatch")))
+      (build-system r-build-system)
+      (propagated-inputs (list r-ggplot2
+                               r-ggpubr
+                               r-gridextra
+                               r-lmertest
+                               r-mixomics
+                               r-mvtnorm
+                               r-performance
+                               r-rdpack
+                               r-scales))
+      (native-inputs (list r-knitr))
+      (home-page "https://github.com/EvaYiwenWang/PLSDAbatch")
+      (synopsis "PLSDA-batch")
+      (description
+       "This package provides a new batch effect correction method based on
+Projection to Latent Structures Discriminant Analysis named “PLSDA-batch” to
+correct data prior to any downstream analysis.  PLSDA-batch estimates latent
+components related to treatment and batch effects to remove batch variation.
+The method is multivariate, non-parametric and performs dimension reduction.
+Combined with centered log ratio transformation for addressing uneven library
+sizes and compositional structure, PLSDA-batch addresses all characteristics
+of microbiome data that existing correction methods have ignored so far.")
+      (license license:gpl3))))
+
 (define-public r-psupertime
   (let ((commit "73825a28d3bd9bc881c15ee0c4c218eec1c9c207")
         (revision "1"))
@@ -8639,6 +8918,62 @@ target genes, Pando simultaneously infers gene modules and sets of regulatory
 regions for each transcription factor.")
     (license license:expat)))
 
+(define-public r-premessa
+  (let ((commit "68b42bb984637d0f3ad6a0ecc83e9278994afc85")
+        (revision "1"))
+    (package
+      (name "r-premessa")
+      (version (git-version "0.3.4" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/ParkerICI/premessa")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "1l0q431zk0lvg22130nx84gdqi7cpl05yah4am63lbx6m4c769pb"))
+                (snippet
+                 '(delete-file "inst/normalizer_shinyGUI/www/d3.min.js"))))
+      (properties `((upstream-name . "premessa")))
+      (build-system r-build-system)
+      (arguments
+       (list
+        #:phases
+        '(modify-phases %standard-phases
+           (add-after 'unpack 'process-javascript
+             (lambda* (#:key inputs #:allow-other-keys)
+               (with-directory-excursion "inst/normalizer_shinyGUI/www/"
+                 (invoke "esbuild" (assoc-ref inputs "d3.v4.js")
+                         "--minify" "--outfile=d3.min.js")))))))
+      (propagated-inputs
+       (list r-data-table
+             r-flowcore
+             r-ggplot2
+             r-gridextra
+             r-hexbin
+             r-jsonlite
+             r-reshape
+             r-rhandsontable
+             r-shiny
+             r-shinyjqui))
+      (native-inputs
+       `(("esbuild" ,esbuild)
+         ("d3.v4.js"
+          ,(origin
+             (method url-fetch)
+             (uri "https://d3js.org/d3.v4.js")
+             (sha256
+              (base32
+               "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
+      (home-page "https://github.com/ParkerICI/premessa")
+      (synopsis "Pre-processing of flow and mass cytometry data")
+      (description
+       "This is an R package for pre-processing of flow and mass cytometry
+data.  This package includes panel editing or renaming for FCS files,
+bead-based normalization and debarcoding.")
+      (license license:gpl3))))
+
 (define-public r-presto
   (let ((commit "052085db9c88aa70a28d11cc58ebc807999bf0ad")
         (revision "0"))
@@ -8730,6 +9065,70 @@ auROC analysis.")
 visualization and analysis of single-cell data using R.")
       (license license:gpl3+))))
 
+(define-public r-markdownhelpers
+  (let ((commit "793372d28ebed607cc1d35f909a1caedb2b41ffe")
+        (revision "1"))
+    (package
+      (name "r-markdownhelpers")
+      (version (git-version "0.2.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/vertesy/MarkdownHelpers")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "1d18s2ydhfjm3hjkxz42dirhwrrv792m6mvkmypallaa2qnwrmkg"))))
+      (properties `((upstream-name . "MarkdownHelpers")))
+      (build-system r-build-system)
+      (propagated-inputs (list r-devtools r-stringendo r-usethis))
+      (home-page "https://github.com/vertesy/MarkdownHelpers")
+      (synopsis "Helper functions for MarkdownReports and ggExpress")
+      (description
+       "This package provides a set of R functions to parse markdown and other
+generic helpers.")
+      (license license:gpl3))))
+
+(define-public r-markdownreports
+  (let ((commit "3ba1103e3ddc6df3a0c090eb884f5e65c461eb31")
+        (revision "1"))
+    (package
+      (name "r-markdownreports")
+      (version (git-version "4.5.9" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/vertesy/MarkdownReports")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "1xmasdb630b6nvxi5m1i8pyxiy49nxpzyxf9h8spdppx92rhdkc8"))))
+      (properties `((upstream-name . "MarkdownReports")))
+      (build-system r-build-system)
+      (propagated-inputs
+       (list r-clipr
+             r-codeandroll2
+             r-colorramps
+             r-devtools
+             r-gplots
+             r-markdownhelpers
+             r-rcolorbrewer
+             r-readwriter
+             r-sessioninfo
+             r-sm
+             r-stringendo
+             r-venndiagram
+             r-vioplot))
+      (home-page "https://github.com/vertesy/MarkdownReports")
+      (synopsis "Tool for generating cientific figures and reports")
+      (description
+       "This is a set of R functions that allows you to generate precise
+figures.  This tool will create clean markdown reports about what you just
+discovered.")
+      (license license:gpl3))))
+
 (define-public r-snapatac
   (package
     (name "r-snapatac")
@@ -8779,6 +9178,30 @@ clustering analysis, differential analysis, motif inference and exploration of
 single cell ATAC-seq sequencing data.")
     (license license:gpl3)))
 
+(define-public r-tictoc
+  (package
+    (name "r-tictoc")
+    (version "1.1")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "tictoc" version))
+              (sha256
+               (base32
+                "0ka7zd857xfqb5afn0psn0yzfv2qjb0ddxfyiq6aggbnla5qc3qj"))))
+    (properties `((upstream-name . "tictoc")))
+    (build-system r-build-system)
+    (home-page "https://github.com/jabiru/tictoc")
+    (synopsis
+     "Time R scripts and implementations of stack and list structures")
+    (description
+     "The tictoc package provides the timing functions @code{tic} and
+@code{toc} that can be nested.  It provides an alternative to
+@code{system.time()} with a different syntax similar to that in another
+well-known software package.  @code{tic} and @code{toc} are easy to use, and
+are especially useful when timing several sections in more than a few lines of
+code.")
+    (license license:asl2.0)))
+
 (define-public r-tsis
   (let ((commit "24460298fbe1d26e4da390f6e4f3d4d9d62334dc")
         (revision "1"))
@@ -15729,6 +16152,60 @@ information...  The package can also be used to extract data from @code{.loom}
 files.")
       (license license:expat))))
 
+(define-public r-seurat-utils
+  (let ((commit "0b6f5b548a49148cfbeaa654e8a618c0a020afa5")
+        (revision "1"))
+    (package
+      (name "r-seurat-utils")
+      (version (git-version "1.6.5" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/vertesy/Seurat.utils")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "1mn64h375mkj6x4ix5493z32gqg96yc507j5jr0lx9g5wk1bf762"))))
+      (properties `((upstream-name . "Seurat.utils")))
+      (build-system r-build-system)
+      (propagated-inputs (list r-codeandroll2
+                               r-cowplot
+                               r-dplyr
+                               r-ggcorrplot
+                               r-ggexpress
+                               r-ggplot2
+                               r-ggpubr
+                               r-ggrepel
+                               r-hgnchelper
+                               r-htmlwidgets
+                               r-markdownhelpers
+                               r-markdownreports
+                               r-matrix
+                               r-matrixstats
+                               r-princurve
+                               r-r-utils
+                               r-readr
+                               r-readwriter
+                               r-reshape2
+                               r-scales
+                               r-seurat
+                               r-soupx
+                               r-sparsematrixstats
+                               r-stringendo
+                               r-stringr
+                               r-tibble
+                               r-tictoc
+                               r-vroom))
+      (home-page "https://github.com/vertesy/Seurat.utils")
+      (synopsis "Collection of utility functions for Seurat")
+      (description
+       "This is a collection of utility functions for Seurat.  These functions
+allow the automation and multiplexing of plotting, 3D plotting, visualization
+of statistics & QC, interaction with the Seurat object.  Some functionalities
+require functions from CodeAndRoll and MarkdownReports libraries.")
+      (license license:gpl3))))
+
 (define-public r-seuratwrappers
   ;; There are no releases or tags.
   (let ((commit "d28512f804d5fe05e6d68900ca9221020d52cf1d")
@@ -17846,7 +18323,6 @@ aligner.")
      (list python-black
            python-flake8
            python-hypothesis
-           python-pre-commit
            python-pytest
            python-setuptools-scm
            python-wheel))