gnu: r-impute: Update to 1.64.0.

[jackhill/guix/guix.git] / gnu / packages / bioinformatics.scm

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 84b036c..586d149 100644 (file)
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7142,14 +7142,14 @@ information as possible.")
 (define-public r-genefilter
   (package
     (name "r-genefilter")
-    (version "1.70.0")
+    (version "1.72.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "genefilter" version))
        (sha256
         (base32
-         "1sbbrnq6p90fri0ik6aq2zw26kasw63nyiy7xkzrj6vgyq7x258g"))))
+         "0929g6c4v2qhgipgrh1a5gv6444sm2dp52x9c3qbk03i8wzc6633"))))
     (build-system r-build-system)
     (native-inputs
      `(("gfortran" ,gfortran)
@@ -7170,14 +7170,14 @@ high-throughput sequencing experiments.")
 (define-public r-deseq2
   (package
     (name "r-deseq2")
-    (version "1.28.1")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DESeq2" version))
        (sha256
         (base32
-         "0xh12c2skr0bbv893p05gvbismkcnqw8zwh7yz4wmycgajfzg2pp"))))
+         "0q2f9cywrcmp1p7ii8f45g4dk4hsnjflq3yqhsxgnpv9fw338qpp"))))
     (properties `((upstream-name . "DESeq2")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7208,14 +7208,14 @@ distribution.")
 (define-public r-dexseq
   (package
     (name "r-dexseq")
-    (version "1.34.1")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DEXSeq" version))
        (sha256
         (base32
-         "1m03awaw06mfv5gszq23k5apsqqzjqa5rcwp20y4xbpl7bywpsyl"))))
+         "0wfjb42xcr4wjy8a654b74411dky8hp6sp8xdwf0sxqgsxy106qi"))))
     (properties `((upstream-name . "DEXSeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7253,14 +7253,14 @@ exploration of the results.")
 (define-public r-annotationforge
   (package
     (name "r-annotationforge")
-    (version "1.30.1")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AnnotationForge" version))
        (sha256
         (base32
-         "1a2155jxbwc6qr3dcyvp850grhdr7czc7bs3s87ff4sgdl0jp3jw"))))
+         "0y3820dkvwz09wlmz9drx6gqpsr9cwppaiz40zafwfxbz65y8px7"))))
     (properties
      `((upstream-name . "AnnotationForge")))
     (build-system r-build-system)
@@ -7285,14 +7285,14 @@ databases.  Packages produced are intended to be used with AnnotationDbi.")
 (define-public r-rbgl
   (package
     (name "r-rbgl")
-    (version "1.64.0")
+    (version "1.66.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RBGL" version))
        (sha256
         (base32
-         "079599a6xn2i7snfn2vgshkw0c00rrfhj44pvi03ap8id29bkayy"))))
+         "016vyzgixb3gjpzi21rbs6ngnnqcxr77krwjjf1ldnzzj8vqrqsz"))))
     (properties `((upstream-name . "RBGL")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7308,14 +7308,14 @@ the graph algorithms contained in the Boost library.")
 (define-public r-gseabase
   (package
     (name "r-gseabase")
-    (version "1.50.1")
+    (version "1.52.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GSEABase" version))
        (sha256
         (base32
-         "1k4faj53cwvqijad8cf7fcghzxcv9shlbpl8n73bsncc8k192y2j"))))
+         "0lcxbxfg62zdf2nql49asn3555cqrrxpjm2xsxf7vlxv84dl6r44"))))
     (properties `((upstream-name . "GSEABase")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7337,14 +7337,14 @@ Enrichment Analysis} (GSEA).")
 (define-public r-category
   (package
     (name "r-category")
-    (version "2.54.0")
+    (version "2.56.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Category" version))
        (sha256
         (base32
-         "1grspdzk5a4vidnxwcd1jmy1vcn494aydsp3vydx235yv7iqac1b"))))
+         "0m77wpnica0h2ia9ajdaiga4plgz1s9wls6pdnxzk7kwl8a68wkr"))))
     (properties `((upstream-name . "Category")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7368,14 +7368,14 @@ analysis.")
 (define-public r-gostats
   (package
     (name "r-gostats")
-    (version "2.54.0")
+    (version "2.56.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GOstats" version))
        (sha256
         (base32
-         "00q39cyv4l28r6s9gjnd0qhl7h80vmwp4lpmchisqzj44xzyics9"))))
+         "18q8p0fv9fl2r6zjxknfjwqxr69dlyxy6c8amzn6c6dwjq1cxk6j"))))
     (properties `((upstream-name . "GOstats")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7399,14 +7399,14 @@ testing and other simple calculations.")
 (define-public r-shortread
   (package
     (name "r-shortread")
-    (version "1.46.0")
+    (version "1.48.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ShortRead" version))
        (sha256
         (base32
-         "0l4kdln69y6yhln0xiv2jmpxg05fjcglln406p43a2bqvk2lr03d"))))
+         "0w4m8d3h660mmr2ymp206r1n4aqssxmkv8yxkbr5y1swrahxzfk9"))))
     (properties `((upstream-name . "ShortRead")))
     (build-system r-build-system)
     (inputs
@@ -7419,6 +7419,7 @@ testing and other simple calculations.")
        ("r-genomeinfodb" ,r-genomeinfodb)
        ("r-genomicalignments" ,r-genomicalignments)
        ("r-genomicranges" ,r-genomicranges)
+       ("r-rhtslib" ,r-rhtslib)
        ("r-hwriter" ,r-hwriter)
        ("r-iranges" ,r-iranges)
        ("r-lattice" ,r-lattice)
@@ -7441,14 +7442,14 @@ ungapped alignment formats.")
 (define-public r-systempiper
   (package
     (name "r-systempiper")
-    (version "1.22.0")
+    (version "1.24.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "systemPipeR" version))
        (sha256
         (base32
-         "01ilhlrvy28jfdyxjria4024yryj5zgympgqznw17g3y3az78kk2"))))
+         "0blvvci57q12sl18yvw07233rfnj47mfadzm0pdpig1ll5z6ld2j"))))
     (properties `((upstream-name . "systemPipeR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7464,6 +7465,7 @@ ungapped alignment formats.")
        ("r-ggplot2" ,r-ggplot2)
        ("r-go-db" ,r-go-db)
        ("r-gostats" ,r-gostats)
+       ("r-iranges" ,r-iranges)
        ("r-limma" ,r-limma)
        ("r-magrittr" ,r-magrittr)
        ("r-pheatmap" ,r-pheatmap)
@@ -7494,14 +7496,14 @@ annotation infrastructure.")
 (define-public r-grohmm
   (package
     (name "r-grohmm")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "groHMM" version))
        (sha256
         (base32
-         "04z9qq1xwdsaxbqhyld37w0ybvzly9pc1hcyrnwdbyjwd7n1fncb"))))
+         "08pap9wsaxl4jjlc1py0rc019gmi6daa0f9cr3ih1d97wybncanx"))))
     (properties `((upstream-name . "groHMM")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7727,13 +7729,13 @@ BLAST, KEGG, GenBank, MEDLINE and GO.")
 (define-public r-biocviews
   (package
     (name "r-biocviews")
-    (version "1.56.2")
+    (version "1.58.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "biocViews" version))
               (sha256
                (base32
-                "0kw0qfm1fw5yv2rbz6x23431rh0fnzj66f2bls7j285biyjmmx7w"))))
+                "0f0aa51h9x8n114zz6q6iw45d78i9wzl4ycbpiy0bdn23167pd84"))))
     (properties
      `((upstream-name . "biocViews")))
     (build-system r-build-system)
@@ -7755,13 +7757,13 @@ also known as views, in a controlled vocabulary.")
 (define-public r-biocstyle
   (package
     (name "r-biocstyle")
-    (version "2.16.1")
+    (version "2.18.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocStyle" version))
               (sha256
                (base32
-                "09sz2bnbfbj8wz16k0q8xrvag9fldxqyp5vbg9pvd9skh28hv7c7"))))
+                "1hfdvld0n9py45mxm05kbb0sq0s9p8yky3s6jb02gzhlxkk3q4fs"))))
     (properties
      `((upstream-name . "BiocStyle")))
     (build-system r-build-system)
@@ -7783,13 +7785,13 @@ functionality.")
 (define-public r-bioccheck
   (package
     (name "r-bioccheck")
-    (version "1.24.0")
+    (version "1.26.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocCheck" version))
               (sha256
                (base32
-                "1p9ys18sn1crxw1iac2jdgqvwpb5hjd9nfxx0qn0ncrv0b550mny"))))
+                "1hyncn9zqj432da95k86rm5b28nbwrvzm52jbhisifkxj1j43cib"))))
     (properties
      `((upstream-name . "BiocCheck")))
     (build-system r-build-system)
@@ -7832,13 +7834,13 @@ checks on R packages that are to be submitted to the Bioconductor repository.")
 (define-public r-s4vectors
   (package
     (name "r-s4vectors")
-    (version "0.26.1")
+    (version "0.28.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "S4Vectors" version))
               (sha256
                (base32
-                "1ddr3ngyczx332zw9ai1a6h7442lgrbfcj8vrhvbkdkzqwj14xmb"))))
+                "0rfn46g2mfda01s75vpcfn5jc7xkp0jrl5v79gyd40jm37p4j1zv"))))
     (properties
      `((upstream-name . "S4Vectors")))
     (build-system r-build-system)
@@ -7859,13 +7861,13 @@ S4Vectors package itself.")
 (define-public r-iranges
   (package
     (name "r-iranges")
-    (version "2.22.2")
+    (version "2.24.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "IRanges" version))
               (sha256
                (base32
-                "1y24jw62806wp2afiyj1x6n00gj7d3323klqdypra9q43pg1w49d"))))
+                "1lfc8xz45v63y3q40im00i944hi0p9idwhx50w3nzkwdpk79315b"))))
     (properties
      `((upstream-name . "IRanges")))
     (build-system r-build-system)
@@ -7911,13 +7913,13 @@ ID and species.  It is used by functions in the GenomeInfoDb package.")
 (define-public r-genomeinfodb
   (package
     (name "r-genomeinfodb")
-    (version "1.24.2")
+    (version "1.26.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomeInfoDb" version))
               (sha256
                (base32
-                "1cqs53p4m5q1dr59war72bccphy01ilw4xra24fmngrv4x32rznd"))))
+                "1xfhz7gmccijy2z015w07lh04g0ijh7zi6k7q6m4lripgban93g9"))))
     (properties
      `((upstream-name . "GenomeInfoDb")))
     (build-system r-build-system)
@@ -7941,13 +7943,13 @@ names in their natural, rather than lexicographic, order.")
 (define-public r-edger
   (package
     (name "r-edger")
-    (version "3.30.3")
+    (version "3.32.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "edgeR" version))
               (sha256
                (base32
-                "1z9bkg08rgqn3jm2s4ndbj641w33wl8jd3j6m5if6h2nnw6011ic"))))
+                "0dkjd6li270icy1x5qbzpakk9bx712mdm5k32lrr3yrggq92jhjg"))))
     (properties `((upstream-name . "edgeR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7969,13 +7971,13 @@ CAGE.")
 (define-public r-variantannotation
   (package
     (name "r-variantannotation")
-    (version "1.34.0")
+    (version "1.36.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "VariantAnnotation" version))
               (sha256
                (base32
-                "09y6ymwky839nb0y7y93w810hk9mvwqn7595q1276c28dkddiqvw"))))
+                "1sl0l6v05lfglj281nszma0h5k234md7rn2pdah8vs2d4iq3kimw"))))
     (properties
      `((upstream-name . "VariantAnnotation")))
     (inputs
@@ -7991,6 +7993,7 @@ CAGE.")
        ("r-genomicfeatures" ,r-genomicfeatures)
        ("r-genomicranges" ,r-genomicranges)
        ("r-iranges" ,r-iranges)
+       ("r-matrixgenerics" ,r-matrixgenerics)
        ("r-summarizedexperiment" ,r-summarizedexperiment)
        ("r-rhtslib" ,r-rhtslib)
        ("r-rsamtools" ,r-rsamtools)
@@ -8008,13 +8011,13 @@ coding changes and predict coding outcomes.")
 (define-public r-limma
   (package
     (name "r-limma")
-    (version "3.44.3")
+    (version "3.46.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "limma" version))
               (sha256
                (base32
-                "09fnqxx4rzq5n447aqg2l6y0idfwgz2jxz99sifxsr2q8afzbcj6"))))
+                "1xxv493q1kip9bjfv7v7k5dnq7hz7gvl80i983v4mvwavhgnbxfz"))))
     (build-system r-build-system)
     (home-page "http://bioinf.wehi.edu.au/limma")
     (synopsis "Package for linear models for microarray and RNA-seq data")
@@ -8063,13 +8066,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.")
 (define-public r-genomicranges
   (package
     (name "r-genomicranges")
-    (version "1.40.0")
+    (version "1.42.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicRanges" version))
               (sha256
                (base32
-                "0wn1zr2qq0rpv9z2wialgizn6xzdlcjg1w2kif67n53svz6vk2x1"))))
+                "0j4py5g6pdj35xhlaqhxxhg55j9l4mcdk3yck4dgyavv5f2dh24i"))))
     (properties
      `((upstream-name . "GenomicRanges")))
     (build-system r-build-system)
@@ -8094,13 +8097,13 @@ manipulating genomic intervals and variables defined along a genome.")
 (define-public r-biobase
   (package
     (name "r-biobase")
-    (version "2.48.0")
+    (version "2.50.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Biobase" version))
               (sha256
                (base32
-                "13p3kgnxm7hbn8cy289kbhaiyfa6rxx7l1pbvajwqzbay3cxznqp"))))
+                "11kgc4flywlm3i18603558l8ksv91c24vkc5fnnbcd375i2dhhd4"))))
     (properties
      `((upstream-name . "Biobase")))
     (build-system r-build-system)
@@ -8116,13 +8119,13 @@ on Bioconductor or which replace R functions.")
 (define-public r-annotationdbi
   (package
     (name "r-annotationdbi")
-    (version "1.50.3")
+    (version "1.52.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AnnotationDbi" version))
               (sha256
                (base32
-                "0qcxfn4pvaksna0nvxr74ysn2wzaxn732pkhd6ffrj8pwhkhy5p3"))))
+                "0zqxgh3nx6y8ry12s2vss2f4axz5vpqxha1y4ifhhcx4zhpzsglr"))))
     (properties
      `((upstream-name . "AnnotationDbi")))
     (build-system r-build-system)
@@ -8145,13 +8148,13 @@ annotation data packages using SQLite data storage.")
 (define-public r-biomart
   (package
     (name "r-biomart")
-    (version "2.44.1")
+    (version "2.46.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "biomaRt" version))
               (sha256
                (base32
-                "0np4nh3gj60mgb6312z7x0z9fg5bhrhw872sp3dzgmqc8q8b84iz"))))
+                "1zpdm8nw1d0m31pdmzw1dccbd6iczfhiklhm4d325zkzf3jrkvxf"))))
     (properties
      `((upstream-name . "biomaRt")))
     (build-system r-build-system)
@@ -8163,7 +8166,8 @@ annotation data packages using SQLite data storage.")
        ("r-progress" ,r-progress)
        ("r-rappdirs" ,r-rappdirs)
        ("r-stringr" ,r-stringr)
-       ("r-xml" ,r-xml)))
+       ("r-xml" ,r-xml)
+       ("r-xml2" ,r-xml2)))
     (native-inputs
      `(("r-knitr" ,r-knitr)))
     (home-page "https://bioconductor.org/packages/biomaRt")
@@ -8182,13 +8186,13 @@ powerful online queries from gene annotation to database mining.")
 (define-public r-biocparallel
   (package
     (name "r-biocparallel")
-    (version "1.22.0")
+    (version "1.24.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocParallel" version))
               (sha256
                (base32
-                "1lsg5xm5j3ly5k60fidzhkgqc9jgscyfkqngjvd9qp6yfzvsb82g"))))
+                "1iryicvmcagcrj29kp49mqhiq2kn72j4idj380hi9illmdrg9ism"))))
     (properties
      `((upstream-name . "BiocParallel")))
     (build-system r-build-system)
@@ -8209,13 +8213,13 @@ objects.")
 (define-public r-biostrings
   (package
     (name "r-biostrings")
-    (version "2.56.0")
+    (version "2.58.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Biostrings" version))
               (sha256
                (base32
-                "0imhfz7dg8b3l5qzipjranqqshdsg2x6zc49drlhn8sc7j40cvi8"))))
+                "1rbqhs73mhfr1gi0rx28jiyan7i3hb45ai3jpl1656fnrhgjfxq5"))))
     (properties
      `((upstream-name . "Biostrings")))
     (build-system r-build-system)
@@ -8236,13 +8240,13 @@ biological sequences or sets of sequences.")
 (define-public r-rsamtools
   (package
     (name "r-rsamtools")
-    (version "2.4.0")
+    (version "2.6.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Rsamtools" version))
               (sha256
                (base32
-                "0z01z0s71f941k7sns46nyabps28c69d6jxx6sppjpc6h4vrw0vq"))))
+                "040pggkwglc6wy90qnc7xcdnaj0v3iqlykvvsl74241409qly554"))))
     (properties
      `((upstream-name . "Rsamtools")))
     (build-system r-build-system)
@@ -8281,13 +8285,13 @@ tab-delimited (tabix) files.")
 (define-public r-delayedarray
   (package
     (name "r-delayedarray")
-    (version "0.14.1")
+    (version "0.16.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "DelayedArray" version))
               (sha256
                (base32
-                "0xi0i621hrl7k9rsc8x8nc3ib74sk8hxhbyr2lxqclw45pk95s7v"))))
+                "1564wnradxw15nsnv6w2wd3xngcs3xa1mlibbq3hygi5fcx4fk3g"))))
     (properties
      `((upstream-name . "DelayedArray")))
     (build-system r-build-system)
@@ -8296,7 +8300,7 @@ tab-delimited (tabix) files.")
        ("r-s4vectors" ,r-s4vectors)
        ("r-iranges" ,r-iranges)
        ("r-matrix" ,r-matrix)
-       ("r-matrixstats" ,r-matrixstats)))
+       ("r-matrixgenerics" ,r-matrixgenerics)))
     (native-inputs
      `(("r-knitr" ,r-knitr)))
     (home-page "https://bioconductor.org/packages/DelayedArray")
@@ -8314,13 +8318,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns),
 (define-public r-summarizedexperiment
   (package
     (name "r-summarizedexperiment")
-    (version "1.18.2")
+    (version "1.20.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "SummarizedExperiment" version))
               (sha256
                (base32
-                "1raw5ycigr6gjgzn3kx3jls5hzww10fhnwd8c17c20hmhirf13rw"))))
+                "04x6d4mcsnvz6glkmf6k2cv3fs8zk03i9rvv0ahpl793n8l411ps"))))
     (properties
      `((upstream-name . "SummarizedExperiment")))
     (build-system r-build-system)
@@ -8332,6 +8336,7 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns),
        ("r-genomicranges" ,r-genomicranges)
        ("r-iranges" ,r-iranges)
        ("r-matrix" ,r-matrix)
+       ("r-matrixgenerics" ,r-matrixgenerics)
        ("r-s4vectors" ,r-s4vectors)))
     (native-inputs
      `(("r-knitr" ,r-knitr)))
@@ -8347,13 +8352,13 @@ samples.")
 (define-public r-genomicalignments
   (package
     (name "r-genomicalignments")
-    (version "1.24.0")
+    (version "1.26.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicAlignments" version))
               (sha256
                (base32
-                "0v8k6d7frm5p48cmk4zik78cw9abz4inx0zhl4zrmmx31ifyvk8d"))))
+                "1q95px6s6snsax4ax955zzpdlrwp5liwf70wqq0lrk9mp6lq0hbr"))))
     (properties
      `((upstream-name . "GenomicAlignments")))
     (build-system r-build-system)
@@ -8380,13 +8385,13 @@ alignments.")
 (define-public r-rtracklayer
   (package
     (name "r-rtracklayer")
-    (version "1.48.0")
+    (version "1.50.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "rtracklayer" version))
               (sha256
                (base32
-                "1zcgk92sidhy4y7ws9ms4nkkh2hnccfhfh53qgna0kma9jy4v5xf"))))
+                "12zimhpdzjyzd81wrzz5hdbzvlgzcs22x1nnaf2jq4cba3ch5px8"))))
     (build-system r-build-system)
     (arguments
      `(#:phases
@@ -8413,7 +8418,8 @@ alignments.")
        ("r-rsamtools" ,r-rsamtools)
        ("r-s4vectors" ,r-s4vectors)
        ("r-xml" ,r-xml)
-       ("r-xvector" ,r-xvector)))
+       ("r-xvector" ,r-xvector)
+       ("r-zlibbioc" ,r-zlibbioc)))
     (home-page "https://bioconductor.org/packages/rtracklayer")
     (synopsis "R interface to genome browsers and their annotation tracks")
     (description
@@ -8427,13 +8433,13 @@ as well as query and modify the browser state, such as the current viewport.")
 (define-public r-genomicfeatures
   (package
     (name "r-genomicfeatures")
-    (version "1.40.1")
+    (version "1.42.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicFeatures" version))
               (sha256
                (base32
-                "0zm7q957g952qyfqmvf27sldsnq6sqd0wlgnqzvmxayg9pxh0l0z"))))
+                "17dyd9hcw6pw16y353dh55wfhxmkxka99lbsxsp9xyrhffwrxi0s"))))
     (properties
      `((upstream-name . "GenomicFeatures")))
     (build-system r-build-system)
@@ -8494,13 +8500,13 @@ information about the latest version of the Gene Ontologies.")
 (define-public r-topgo
   (package
     (name "r-topgo")
-    (version "2.40.0")
+    (version "2.42.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "topGO" version))
               (sha256
                (base32
-                "13rhbvn27sj75fklf1cnjaazacx8yyjlhqlnbp5zk157q6y5cwdr"))))
+                "0vr3l9gvd3dhy446k3fkj6rm7z1abxi56rbnrs64297yzxaz1ngl"))))
     (properties
      `((upstream-name . "topGO")))
     (build-system r-build-system)
@@ -8527,13 +8533,13 @@ dependencies between GO terms can be implemented and applied.")
 (define-public r-bsgenome
   (package
     (name "r-bsgenome")
-    (version "1.56.0")
+    (version "1.58.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BSgenome" version))
               (sha256
                (base32
-                "1jw8r1qm9fpg2s1cw2y4np243jjxm65j2xdy2785h8fc1b02msf6"))))
+                "1gbvmxr6r57smgvhqgwspbcnwyk4hsfkxkpzzcs6470q03zfb4wq"))))
     (properties
      `((upstream-name . "BSgenome")))
     (build-system r-build-system)
@@ -8558,13 +8564,13 @@ genome data packages and support for efficient SNP representation.")
 (define-public r-impute
   (package
     (name "r-impute")
-    (version "1.62.0")
+    (version "1.64.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "impute" version))
               (sha256
                (base32
-                "161p6l1cp3wwdynkxwvg0yhrh6yv20brdlplw5w5mavn4hf1nm0h"))))
+                "1pnjasw9i19nmxwjzrd9jbln31yc5jilfvwk414ya5zbqfsazvxa"))))
     (native-inputs
      `(("gfortran" ,gfortran)))
     (build-system r-build-system)