Merge remote-tracking branch 'origin/master' into wip-guile-ssh-0.16

1 files changed, 84 insertions, 89 deletions

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 29768dc7c2..53c7d048c9 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2334,13 +2334,13 @@ analysis, modelling, and visualization of spike-in controls.")
 (define-public r-ancombc
   (package
     (name "r-ancombc")
-    (version "2.0.1")
+    (version "2.0.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "ANCOMBC" version))
               (sha256
                (base32
-                "1bwzvi6j3s66dcll1lb4xy25j4nfn1ln6mc3flh0wgy13l26x8m6"))))
+                "0dlinv4vhxgni8ygzvfw8pbc6d1v9x5chhrpxblhs2c65bkgyxz5"))))
     (properties `((upstream-name . "ANCOMBC")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3292,13 +3292,13 @@ Various visual and textual types of output are available.")
 (define-public r-bambu
   (package
     (name "r-bambu")
-    (version "3.0.2")
+    (version "3.0.5")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "bambu" version))
               (sha256
                (base32
-                "0246cn5l1kxysjrzy4prfdxn71vc47a8kciqw384nm2mi3vsy4vx"))))
+                "12rcbspy4ly714cyxbgd5v2m92vasksxm19m6hd4avasrhcr4d6l"))))
     (properties `((upstream-name . "bambu")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3335,13 +3335,13 @@ usage.")
 (define-public r-bandits
   (package
     (name "r-bandits")
-    (version "1.14.0")
+    (version "1.14.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BANDITS" version))
               (sha256
                (base32
-                "18xq8gg1j07gbbxy7r0cc34zwn40mh4fr39zzi8l3z0cymw73qs8"))))
+                "0dbiz7zgdl3bqrwf4ffb73sc2dd8ygh76fakx5887a14azj8pk8x"))))
     (properties `((upstream-name . "BANDITS")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3600,13 +3600,13 @@ factorial microarray data.")
 (define-public r-damefinder
   (package
     (name "r-damefinder")
-    (version "1.10.0")
+    (version "1.10.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "DAMEfinder" version))
               (sha256
                (base32
-                "0ygsgg51473sycsh367rf8plca6zb1jg2l39zcprwvgpiln8mjdg"))))
+                "1cgykb70mxnhilwwp1jr4dr523zvjxpix173s4ldfh49064gzwc1"))))
     (properties `((upstream-name . "DAMEfinder")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3914,13 +3914,13 @@ negative control samples.")
 (define-public r-deconvr
   (package
     (name "r-deconvr")
-    (version "1.4.2")
+    (version "1.4.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "deconvR" version))
               (sha256
                (base32
-                "1wa8l9zxdwx32122slnzqyk32klyznxnbziwn98jbp5fxmjka92l"))))
+                "1jz7q4rv3m85bcvarjhqsyc2330fynb0wr5ajd2qffznczk846xb"))))
     (properties `((upstream-name . "deconvR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3936,6 +3936,7 @@ negative control samples.")
            r-mass
            r-matrixstats
            r-methylkit
+           r-minfi
            r-nnls
            r-quadprog
            r-rsq
@@ -4996,13 +4997,13 @@ only one command.")
 (define-public r-biocparallel
   (package
     (name "r-biocparallel")
-    (version "1.32.3")
+    (version "1.32.4")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocParallel" version))
               (sha256
                (base32
-                "0z2g3p6ip4g865na9bmqaa7w2s52769pmjr3hpiv6x8bhifh3nm5"))))
+                "1m4i27zx3ajwygwp38lrxf36rs575dkaxxc6jawpj1kzn7whi5ym"))))
     (properties
      `((upstream-name . "BiocParallel")))
     (build-system r-build-system)
@@ -5363,26 +5364,26 @@ distribution.")
 (define-public r-deseq2
   (package
     (name "r-deseq2")
-    (version "1.38.1")
+    (version "1.38.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DESeq2" version))
        (sha256
         (base32
-         "0xp3rfhwn8k1bqzqnjzjqlaq8lqyad7kqjhb29vkbxgzjvafvxmk"))))
+         "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
@@ -5595,13 +5596,13 @@ global-scaling and full-quantile normalization.")
 (define-public r-edger
   (package
     (name "r-edger")
-    (version "3.40.0")
+    (version "3.40.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "edgeR" version))
               (sha256
                (base32
-                "18vap3qp9blncr4sdl9q1szb4qhm46gldhxy3k3abw9fckcvggwg"))))
+                "1a0rmczlqmqmip2ix28m4iwcpfj04p6nrcl562bjgaifvgyjqhzg"))))
     (properties `((upstream-name . "edgeR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5720,14 +5721,14 @@ analysis using other methods.")
 (define-public r-genefilter
   (package
     (name "r-genefilter")
-    (version "1.80.0")
+    (version "1.80.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "genefilter" version))
        (sha256
         (base32
-         "0swdqdyz956gx44crbx3qai0qx7n7yazg3yw7i93djcgahyz3kk7"))))
+         "0f25z0hqmrkimv14j03pgjsxpq5rz9ymk151rlg4j4vpc06n73cq"))))
     (build-system r-build-system)
     (native-inputs
      (list gfortran r-knitr))
@@ -5810,13 +5811,13 @@ genomic intervals.  In addition, it can use BAM or BigWig files as input.")
 (define-public r-genomeinfodb
   (package
     (name "r-genomeinfodb")
-    (version "1.34.3")
+    (version "1.34.4")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomeInfoDb" version))
               (sha256
                (base32
-                "1pw8ml6b33z7zh7h592xl23l8dy32nqq4lzq20p57n9f0krqj1iv"))))
+                "1nskqmlar85zg96c1fbacl7dqg6r0gl814rc7yh482y4wgmwyg0r"))))
     (properties
      `((upstream-name . "GenomeInfoDb")))
     (build-system r-build-system)
@@ -5870,13 +5871,13 @@ alignments.")
 (define-public r-genomicfeatures
   (package
     (name "r-genomicfeatures")
-    (version "1.50.2")
+    (version "1.50.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicFeatures" version))
               (sha256
                (base32
-                "10w15j107hy9qb0lh6jmyw7rinfvy3ca34xsskxw3wf25mh6vhzz"))))
+                "14pn7lngayascj5k84g2g748assbivpiakss247cdj9ngzx5sfwz"))))
     (properties
      `((upstream-name . "GenomicFeatures")))
     (build-system r-build-system)
@@ -5948,13 +5949,13 @@ provide added flexibility for data combination and manipulation.")
 (define-public r-genomicranges
   (package
     (name "r-genomicranges")
-    (version "1.50.1")
+    (version "1.50.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicRanges" version))
               (sha256
                (base32
-                "14m4pvvd9m8kpc7k905km9vib7giq0i9g11bxc1ygw30ifi96966"))))
+                "13b6bm6nrxx1vgzrzpf59c2lq5w8kjq9hsch5h037f0p9w3w5z9p"))))
     (properties
      `((upstream-name . "GenomicRanges")))
     (build-system r-build-system)
@@ -6111,13 +6112,13 @@ of other R packages who wish to make use of HTSlib.")
 (define-public r-impute
   (package
     (name "r-impute")
-    (version "1.72.1")
+    (version "1.72.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "impute" version))
               (sha256
                (base32
-                "0862mpbmznizcq5bgnp85dl9q0bip76jkga45gssdrv90wsi2192"))))
+                "1k697pqlkrwmfszipl9irbzmwhk1vz97j3rh0k5nj2mrj3dr71mv"))))
     (native-inputs
      (list gfortran))
     (build-system r-build-system)
@@ -6180,13 +6181,13 @@ Shiny-based display methods for Bioconductor objects.")
 (define-public r-lfa
   (package
     (name "r-lfa")
-    (version "1.28.0")
+    (version "1.28.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "lfa" version))
        (sha256
-        (base32 "1l3ip0bsvbz9nagzv47qjh5hf7qf8ffk4hlnkwagngiwyq84vyp1"))))
+        (base32 "0047wspvarbnbawrwvfjfz5y6i36l2r2k2501zjya09rjpiq101m"))))
     (properties `((upstream-name . "lfa")))
     (build-system r-build-system)
     (propagated-inputs (list r-corpcor))
@@ -7313,13 +7314,13 @@ comprehensive scDblFinder method.")
 (define-public r-scmap
   (package
     (name "r-scmap")
-    (version "1.20.0")
+    (version "1.20.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scmap" version))
        (sha256
-        (base32 "14vyjvfs2n4h0xsy25xg4zdmc8dqbg5vyl3qns6f0rh4bsshqdlm"))))
+        (base32 "0rq185ynk874vgw4a5s2n92381dj6kxxnx2fcx2v7b2ahr3ybys7"))))
     (properties `((upstream-name . "scmap")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7860,13 +7861,13 @@ dependencies between GO terms can be implemented and applied.")
 (define-public r-tximport
   (package
     (name "r-tximport")
-    (version "1.26.0")
+    (version "1.26.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "tximport" version))
               (sha256
                (base32
-                "1w1m6r85a5nvcfxbkq5dmczaar8vf3vbrgrmxqkjqhlpcq58z5ng"))))
+                "1r67q4nb2bx9nqycyr2gnfmh4gizl0c7l510vmlcdvplv3yi73yn"))))
     (build-system r-build-system)
     (native-inputs
      (list r-knitr))
@@ -8233,14 +8234,14 @@ packages.")
 (define-public r-oligo
   (package
     (name "r-oligo")
-    (version "1.62.0")
+    (version "1.62.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "oligo" version))
        (sha256
         (base32
-         "0l6yb58frh4c080k6h8wyipc5kiz4qi7jimnr62jg8d737rrvnk2"))))
+         "1rhzav57d092ip9qjsmskj3l8h4xyq8cpa2a2jl8g32fwh0dyvsz"))))
     (properties `((upstream-name . "oligo")))
     (build-system r-build-system)
     (inputs (list zlib))
@@ -8378,14 +8379,14 @@ signal in the input, that lead to spurious peaks during peak calling.")
 (define-public r-diffbind
   (package
     (name "r-diffbind")
-    (version "3.8.1")
+    (version "3.8.3")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DiffBind" version))
        (sha256
         (base32
-         "1wgnrd1xpl49pdxxjzzl0v9535naapwp3ayqzvrx3z4m6iai2awj"))))
+         "039gy9ll6ingh3y5h2hp3rhbh2imaryjxzgf8ysk87irlbpnx1qs"))))
     (properties `((upstream-name . "DiffBind")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9096,13 +9097,13 @@ information.")
 (define-public r-glmgampoi
   (package
     (name "r-glmgampoi")
-    (version "1.10.0")
+    (version "1.10.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "glmGamPoi" version))
               (sha256
                (base32
-                "12jbqigg4k2ngrk2anbrrxrwkp57bbzdz492lg8lc6w1gygp5yip"))))
+                "1qxzbh5i208cpghmysailachj8xpx4g4iqk8552xjpjkn54pkpbd"))))
     (properties `((upstream-name . "glmGamPoi")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9623,14 +9624,14 @@ penalized least squares regression method.")
 (define-public r-dnacopy
   (package
     (name "r-dnacopy")
-    (version "1.72.0")
+    (version "1.72.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DNAcopy" version))
        (sha256
         (base32
-         "0z2hl68f5f6d2w6gbhax4531g3zbgiihj99h32sa44hp29al38ld"))))
+         "1f6ilfwhli7bdnr48y2ijdydvw7kjbyz701kgbsw3w7inr6x6ayr"))))
     (properties `((upstream-name . "DNAcopy")))
     (build-system r-build-system)
     (native-inputs (list gfortran))
@@ -9781,14 +9782,14 @@ coordinates.")
 (define-public r-lpsymphony
   (package
     (name "r-lpsymphony")
-    (version "1.26.0")
+    (version "1.26.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "lpsymphony" version))
        (sha256
         (base32
-         "0ryl48zxscb35s1gizyspxg48dlqg1j51h9iw2flq16y7y63ppzi"))))
+         "167zpf7k7gn7gw2cxkqx89y322qinyzjr1naracp5axj4q2qagm3"))))
     (build-system r-build-system)
     (arguments
      (list
@@ -10670,14 +10671,14 @@ especially Illumina Infinium methylation microarrays.")
 (define-public r-linnorm
   (package
     (name "r-linnorm")
-    (version "2.22.0")
+    (version "2.22.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Linnorm" version))
        (sha256
         (base32
-         "0ndhvdd9gkqyayxqgj5320sgj15di7ji945lpdi3rj5lwldh7na0"))))
+         "16d7viyidqbsy3mbr2cpq9p291yf362a4blhvs05qxcwm3fjllij"))))
     (properties `((upstream-name . "Linnorm")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11018,14 +11019,14 @@ the data set is suitable for such analysis.")
 (define-public r-sigpathway
   (package
     (name "r-sigpathway")
-    (version "1.66.0")
+    (version "1.66.1")
     (source
       (origin
         (method url-fetch)
         (uri (bioconductor-uri "sigPathway" version))
         (sha256
           (base32
-            "0vb6v61ak8z3hx7d65lr1hrxk89n36j0zi3x0pp828khdyh3zvag"))))
+            "1ln1n4zwmjw1ils45vix93q3h19xlg4q894yhhxkphgyj0qcy00b"))))
     (properties `((upstream-name . "sigPathway")))
     (build-system r-build-system)
     (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
@@ -11140,14 +11141,14 @@ data.")
 (define-public r-enrichplot
   (package
     (name "r-enrichplot")
-    (version "1.18.1")
+    (version "1.18.3")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "enrichplot" version))
        (sha256
         (base32
-         "1x84wlkqisq1x2zniy4mp02zlsp4v85kxbflalmq0pixlkagq0vr"))))
+         "0nzcr23m58z3h0n0frxf26z14j7ilcl4fjy7rqm7f2i1wyld70zl"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-aplot
@@ -11218,13 +11219,13 @@ profiles (GO and KEGG) of gene and gene clusters.")
 (define-public r-clusterexperiment
   (package
     (name "r-clusterexperiment")
-    (version "2.18.0")
+    (version "2.18.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "clusterExperiment" version))
               (sha256
                (base32
-                "04kdiwz8qzr7cr1an1c7a684wqv9pkca0iaym5f069pdjhqvvq0a"))))
+                "1f3f56d88yiqyj45rhcwqb04wbxr9m4fxhbbckw1j7nykm8100ps"))))
     (build-system r-build-system)
     (native-inputs
      (list r-knitr))
@@ -11987,14 +11988,14 @@ investigation using RNA-seq data.")
 (define-public r-aucell
   (package
     (name "r-aucell")
-    (version "1.20.1")
+    (version "1.20.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AUCell" version))
        (sha256
         (base32
-         "0bq729kavqkam2s4dmfzixgznsys61j0lvj5pk3b70gxv44gmpsh"))))
+         "1qb13qd5xzgrpx6jlg3ll0ff5spz3y06ji31vvqzm759almg2w3s"))))
     (properties `((upstream-name . "AUCell")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12003,6 +12004,7 @@ investigation using RNA-seq data.")
            r-delayedarray
            r-delayedmatrixstats
            r-gseabase
+           r-matrix
            r-mixtools
            r-r-utils
            r-shiny
@@ -12823,14 +12825,14 @@ and data files used across sessions.")
 (define-public r-iclusterplus
   (package
     (name "r-iclusterplus")
-    (version "1.34.0")
+    (version "1.34.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "iClusterPlus" version))
        (sha256
         (base32
-         "01bl1gmc1v1b4lh88sdazjvm8pl7383dgzxnhmzpxwz7lkcxi1h2"))))
+         "05y4jmbf8sxl32f3g5lw9ycxky0rw69gax3n2z0kif7xcb5qf3qv"))))
     (properties `((upstream-name . "iClusterPlus")))
     (build-system r-build-system)
     (native-inputs (list gfortran))
@@ -13263,14 +13265,14 @@ annotations.")
 (define-public r-rsubread
   (package
     (name "r-rsubread")
-    (version "2.12.0")
+    (version "2.12.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rsubread" version))
        (sha256
         (base32
-         "0iha7xln7l3mrmka8rcmmlp74f5km9rc88k9nv6bxw0krr03089n"))))
+         "1gvd8vmglvzc3bixqxrm4k7yikl2as5l4x6bvvvnwsgx2i7vz7dm"))))
     (properties `((upstream-name . "Rsubread")))
     (build-system r-build-system)
     (inputs (list zlib))
@@ -13496,14 +13498,14 @@ manipulation of flow cytometry data.")
 (define-public r-ggcyto
   (package
     (name "r-ggcyto")
-    (version "1.26.0")
+    (version "1.26.4")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ggcyto" version))
        (sha256
         (base32
-         "0phhm54wcqihj62a0jk46whmf6wwg7wj3306wvnszy7yik4z857w"))))
+         "1pj1v0bhvckvwn1p826phskqz9lv71c1913cz5w0fd87dzdbpzpj"))))
     (properties `((upstream-name . "ggcyto")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13719,38 +13721,30 @@ package.")
 (define-public r-opencyto
   (package
     (name "r-opencyto")
-    (version "2.10.0")
+    (version "2.10.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "openCyto" version))
        (sha256
         (base32
-         "1pkpm98fs17zqdvyymd58sl4cib7gdi7drvdkagilrafjcrpq31m"))))
+         "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")
@@ -13950,14 +13944,14 @@ data, to only emphasize the data that actually matters.")
 (define-public r-rcistarget
   (package
     (name "r-rcistarget")
-    (version "1.17.0")
+    (version "1.18.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RcisTarget" version))
        (sha256
         (base32
-         "1anwin5476q2n0zgywrmp3nj6sgy07i6pw1lczydvn4h1a8n1rvk"))))
+         "02lz2m2zhwy1dvmjvlss6qg0dh574qhnvn7al3wx7ck1hkz0dgi2"))))
     (properties `((upstream-name . "RcisTarget")))
     (build-system r-build-system)
     (propagated-inputs
@@ -15620,13 +15614,13 @@ functionality.")
 (define-public r-biocviews
   (package
     (name "r-biocviews")
-    (version "1.66.0")
+    (version "1.66.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "biocViews" version))
               (sha256
                (base32
-                "1rgn0agw5m4y8838lxzq1r658h1pblaidmm444yfimjffa8znj23"))))
+                "1xplkzm29v6aysfhb6kf2nnmvc37jmcvv6vsgbx8z8qccn96jk02"))))
     (properties
      `((upstream-name . "biocViews")))
     (build-system r-build-system)
@@ -15638,6 +15632,7 @@ 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
@@ -16206,14 +16201,14 @@ generated.")
 (define-public r-preprocesscore
   (package
     (name "r-preprocesscore")
-    (version "1.60.0")
+    (version "1.60.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "preprocessCore" version))
        (sha256
         (base32
-         "1l0m591scln024jdpib47fndhx2wfp9jgkj3mdmwd9nkc5y0qjda"))))
+         "1rwr31jp4dh3xcfx1kx8rz5xvyx1mrwy85hqrjrfr4m6h0qv28k1"))))
     (properties
      `((upstream-name . "preprocessCore")))
     (build-system r-build-system)
@@ -16227,13 +16222,13 @@ routines.")
 (define-public r-s4vectors
   (package
     (name "r-s4vectors")
-    (version "0.36.0")
+    (version "0.36.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "S4Vectors" version))
               (sha256
                (base32
-                "05al4diwdbsa9b37i8msxnp79fxk7k24dk2vhh131s3snb89jvfs"))))
+                "16lssnmhy3klqp4sw1328f38cixkjh9317gdyikcrmsbcwg2ak6v"))))
     (properties
      `((upstream-name . "S4Vectors")))
     (build-system r-build-system)
@@ -16717,13 +16712,13 @@ This package wraps C++ code from the MOODS motif calling library.")
 (define-public r-chromvar
   (package
     (name "r-chromvar")
-    (version "1.20.0")
+    (version "1.20.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "chromVAR" version))
        (sha256
-        (base32 "1rwgbicbmszdkr05ksxfsisyhk0a4pvc3jrxbzjyc13jj5h6m5kp"))))
+        (base32 "1nhhpqhpvmw6b0nwxdwsjnakmfpxzpii8fmabwwg9bk8ni3zj5dq"))))
     (properties `((upstream-name . "chromVAR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -16824,14 +16819,14 @@ cell types to infer the cell of origin of each single cell independently.")
 (define-public r-scuttle
   (package
     (name "r-scuttle")
-    (version "1.8.1")
+    (version "1.8.3")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scuttle" version))
        (sha256
         (base32
-         "10wk46zgi57m9q9ab6wlmljcss3fph2r9yp1bp01s9yv7sd749b2"))))
+         "1wgh28rj8m5dz89s9y4rzfy68d8ign6pcnnwj9g7h4sc3jfsg56i"))))
     (properties `((upstream-name . "scuttle")))
     (build-system r-build-system)
     (propagated-inputs
@@ -16904,14 +16899,14 @@ quality control.")
 (define-public r-scran
   (package
     (name "r-scran")
-    (version "1.26.0")
+    (version "1.26.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scran" version))
        (sha256
         (base32
-         "11iwpw44600pfx01vqil97k728m1wf4dljr27k2ak4s7z75kxfih"))))
+         "1sqc8pf1qzm24kf1l45da12wbzv0nxsy6l3v9fc8srmnvk37p04p"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-beachmat
@@ -17506,13 +17501,13 @@ EMBL-EBI GWAS catalog.")
 (define-public r-kegggraph
   (package
     (name "r-kegggraph")
-    (version "1.58.0")
+    (version "1.58.3")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "KEGGgraph" version))
        (sha256
-        (base32 "0hpsb009qmhy9p67d5wd0cl60smhgjlhxsz5f52i1c6qy4jk1niq"))))
+        (base32 "1s5j7zdp8ck4vhca81i4b6qclhwi56gmz8brawrxj3szvwmxf3y6"))))
     (properties `((upstream-name . "KEGGgraph")))
     (build-system r-build-system)
     (propagated-inputs