gnu: r-plgem: Update to 1.62.0.

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

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index b8cdcbc..05336e9 100644 (file)
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2,7 +2,7 @@
 ;;; Copyright © 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
-;;; Copyright © 2019 Simon Tournier <zimon.toutoune@gmail.com>
+;;; Copyright © 2019, 2020 Simon Tournier <zimon.toutoune@gmail.com>
 ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
 ;;; Copyright © 2020 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
@@ -748,13 +748,13 @@ annotations.")
 (define-public r-ideoviz
   (package
     (name "r-ideoviz")
-    (version "1.24.0")
+    (version "1.26.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "IdeoViz" version))
               (sha256
                (base32
-                "1ndj14qhpgidjb4qsga80ghqzz1x8kvy2gy1bvvgwlkfxa62rn50"))))
+                "1k5c0skr6pvpcvkak9f0a088w5wsx4fl3jb9a76gyyni4nkj7djq"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biobase" ,r-biobase)
@@ -1077,13 +1077,13 @@ package @code{affy}.")
 (define-public r-coverageview
   (package
     (name "r-coverageview")
-    (version "1.26.0")
+    (version "1.28.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "CoverageView" version))
               (sha256
                (base32
-                "1fcz7pkffz5l3jdxb9glji2zdmr6nx67h6vfpr2yi8n3slg2hrrj"))))
+                "1k89gzqhd8ca8s9gk5bfzringnc5nayqbwzwwy35fls1cg96qmsj"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-s4vectors" ,r-s4vectors)
@@ -1104,13 +1104,13 @@ how the coverage distributed across the genome.")
 (define-public r-cummerbund
   (package
    (name "r-cummerbund")
-   (version "2.30.0")
+   (version "2.32.0")
    (source (origin
              (method url-fetch)
              (uri (bioconductor-uri "cummeRbund" version))
              (sha256
               (base32
-               "1av7yfxcq1wwbqfqcz7caiz5kf6kg5wq9qcg5v6yccihclzwvxjc"))))
+               "1x7rby50api1c66al6a0i92q82ydjmh3h8l2k7hj0ffpn8c5pdgj"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-biobase" ,r-biobase)
@@ -1170,14 +1170,14 @@ across the entire multi-'omics experiment.")
 (define-public r-biocversion
   (package
     (name "r-biocversion")
-    (version "3.11.1")
+    (version "3.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocVersion" version))
        (sha256
         (base32
-         "1rrzx3dqds0jlj1bmjc744wiamb2hssbh3jfxz1s9jp4cvnwrpmz"))))
+         "1cj9swyf4zbkdq45bhw0kymh2aghkwimxjlfj5r2j7kdiyh6n3rk"))))
     (properties `((upstream-name . "BiocVersion")))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/BiocVersion/")
@@ -1190,13 +1190,13 @@ of Bioconductor.")
 (define-public r-biocgenerics
   (package
     (name "r-biocgenerics")
-    (version "0.34.0")
+    (version "0.36.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocGenerics" version))
               (sha256
                (base32
-                "15nvqyh2gx5zkn1krbs5c4rhw5642bijdfsf2rgic70gzr05cksk"))))
+                "1y9pgangz2f0n9v3zj8brz8bv7a1yjsncdnd5h1l7zv0c0j9fh9q"))))
     (properties
      `((upstream-name . "BiocGenerics")))
     (build-system r-build-system)
@@ -1210,14 +1210,14 @@ packages.")
 (define-public r-affycomp
   (package
     (name "r-affycomp")
-    (version "1.64.0")
+    (version "1.66.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affycomp" version))
        (sha256
         (base32
-         "0zg8dshas5b2ny4pnxxxqihnr4l20666ivrgglb939a23mplgps0"))))
+         "106gz4rami04r0ffc7rxkrv92s3yrcnlqnyykd5s8lrkndbihrpk"))))
     (properties `((upstream-name . "affycomp")))
     (build-system r-build-system)
     (propagated-inputs `(("r-biobase" ,r-biobase)))
@@ -1231,14 +1231,14 @@ measures for Affymetrix Oligonucleotide Arrays.")
 (define-public r-affycompatible
   (package
     (name "r-affycompatible")
-    (version "1.48.0")
+    (version "1.50.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AffyCompatible" version))
        (sha256
         (base32
-         "0394sr4spafhfypjsafwjr0y0zsgv52ajdcyvsmkdk7375898lqd"))))
+         "0pcs51miy45bky26i1d4iarbjh569gssb5g4fr26bzgjmq19yl7x"))))
     (properties
      `((upstream-name . "AffyCompatible")))
     (build-system r-build-system)
@@ -1259,14 +1259,14 @@ Command Console} (AGCC)-compatible sample annotation files.")
 (define-public r-affycontam
   (package
     (name "r-affycontam")
-    (version "1.46.0")
+    (version "1.48.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affyContam" version))
        (sha256
         (base32
-         "1dh5c3blk2dl9kg13y6snplnx61x2f9hvp5lc7jmg25xk916517i"))))
+         "0pi5fll5868sb80vb9kbymz6gkjv58f0abk6zwn407cnyjhr342b"))))
     (properties `((upstream-name . "affyContam")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1284,14 +1284,14 @@ problems in CEL-level data to help evaluate performance of quality metrics.")
 (define-public r-affycoretools
   (package
     (name "r-affycoretools")
-    (version "1.60.1")
+    (version "1.62.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affycoretools" version))
        (sha256
         (base32
-         "0cnb54b3kmg9rnycvaz949bdali9n98qzrw7gwka6abmg1lv232s"))))
+         "0jacgwylg7wjw3xk3ga2sb1wkdklm5glamhbmqgvzm5kdjnl0rv0"))))
     (properties `((upstream-name . "affycoretools")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1326,14 +1326,14 @@ to streamline the more common analyses that a Biostatistician might see.")
 (define-public r-affxparser
   (package
     (name "r-affxparser")
-    (version "1.60.0")
+    (version "1.62.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affxparser" version))
        (sha256
         (base32
-         "0d4hq1w0a3dm4bg9qsv7wqrbv2y7b9gllxfmnqs9n2nnwmvgi8yq"))))
+         "13h4iwskvgwgxid9f60gzb1zndgbhdlbn9ixv5waihy1jkcbn24p"))))
     (properties `((upstream-name . "affxparser")))
     (build-system r-build-system)
     (home-page "https://github.com/HenrikBengtsson/affxparser")
@@ -1354,21 +1354,21 @@ structure.")
 (define-public r-annotate
   (package
     (name "r-annotate")
-    (version "1.66.0")
+    (version "1.68.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "annotate" version))
        (sha256
         (base32
-         "1ivszqknryq6n5a85z8zj12fvgcs6zz3zlza8q08pl6cs4m5rm4w"))))
+         "1rql591x56532m8n4axdkfkhkbcsz5hfrf7271s0lmkvy84i7z6l"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
        ("r-biobase" ,r-biobase)
        ("r-biocgenerics" ,r-biocgenerics)
        ("r-dbi" ,r-dbi)
-       ("r-rcurl" ,r-rcurl)
+       ("r-httr" ,r-httr)
        ("r-xml" ,r-xml)
        ("r-xtable" ,r-xtable)))
     (home-page
@@ -1381,14 +1381,14 @@ microarrays.")
 (define-public r-hpar
   (package
     (name "r-hpar")
-    (version "1.30.0")
+    (version "1.32.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "hpar" version))
        (sha256
         (base32
-         "1jq0qw7wq3426cp004divywjm3ryixkykcmwlhrri13agz6rx3r9"))))
+         "0h10b0fyblpsnxj60rpbk99z7snrkkb5jssmf0v27s6d445jq2zr"))))
     (build-system r-build-system)
     (native-inputs
      `(("r-knitr" ,r-knitr)))
@@ -1401,14 +1401,14 @@ the Human Protein Atlas project.")
 (define-public r-regioner
   (package
     (name "r-regioner")
-    (version "1.20.1")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "regioneR" version))
        (sha256
         (base32
-         "0bzjwzj5mvb49wgvs3gd3jfpm7s0zfkca763i65i7m994lgvz33c"))))
+         "0c2khfyrgy3y68cj6b07s91hplabbj70xwdgwrf2bsd9h6gknjdi"))))
     (properties `((upstream-name . "regioneR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1432,14 +1432,14 @@ region sets and other genomic features.")
 (define-public r-reportingtools
   (package
     (name "r-reportingtools")
-    (version "2.28.0")
+    (version "2.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ReportingTools" version))
        (sha256
         (base32
-         "1ig1h224silbdbdr0j9j9sysp9l9dzpcsjzn8jp57h3gh4pdqbfx"))))
+         "0gkshdhx44yjffqf1xmvik7j5hlhszp1n9ckanaws9ky3iia8j31"))))
     (properties
      `((upstream-name . "ReportingTools")))
     (build-system r-build-system)
@@ -1482,14 +1482,14 @@ browser.")
 (define-public r-geneplotter
   (package
     (name "r-geneplotter")
-    (version "1.66.0")
+    (version "1.68.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "geneplotter" version))
        (sha256
         (base32
-         "1y494da1llmrvn3qm7akwgwjazvpffabi8llw3fbday14cay1br5"))))
+         "1f8nr60n1nig1gdy85wqdhpzxvp9r4chygxm8xpy882mdvfv6rqx"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotate" ,r-annotate)
@@ -1507,14 +1507,14 @@ browser.")
 (define-public r-oligoclasses
   (package
     (name "r-oligoclasses")
-    (version "1.50.4")
+    (version "1.52.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "oligoClasses" version))
        (sha256
         (base32
-         "1d8c3i8v8kcm1afgpz6zc1iysip7993y8456cqxl37f7n6n0ax67"))))
+         "19p6h0cgnma5md5mm9bn6rxfhr0a9znljgdbvsqybms6asvh18gy"))))
     (properties `((upstream-name . "oligoClasses")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1542,14 +1542,14 @@ packages.")
 (define-public r-oligo
   (package
     (name "r-oligo")
-    (version "1.52.1")
+    (version "1.54.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "oligo" version))
        (sha256
         (base32
-         "1gpvr33pwzz1glzajcipvjcplb7yxvjj00q0ybqcc3wa47bhfkwd"))))
+         "0cpfkvxpni7an361li0k0qlfcraj7z9zv71r25dbly5kp3dql7k3"))))
     (properties `((upstream-name . "oligo")))
     (build-system r-build-system)
     (inputs `(("zlib" ,zlib)))
@@ -1578,14 +1578,14 @@ Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
 (define-public r-qvalue
   (package
     (name "r-qvalue")
-    (version "2.20.0")
+    (version "2.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "qvalue" version))
        (sha256
         (base32
-         "1hndmdr9niagbr4ry0vbhffvjzjg9im27kdbn0sa774k6r5b4z3f"))))
+         "0xbww16lz0k2p4mmq1aqd7iz7d8rvzgw1gm55jy6xbx19ymj64i5"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-ggplot2" ,r-ggplot2)
@@ -1606,32 +1606,112 @@ problems in genomics, brain imaging, astrophysics, and data mining.")
     ;; Any version of the LGPL.
     (license license:lgpl3+)))
 
+(define r-rcppnumerical
+  (package
+   (name "r-rcppnumerical")
+   (version "0.4-0")
+   (source (origin
+            (method url-fetch)
+            (uri (cran-uri "RcppNumerical" version))
+            (sha256
+             (base32
+              "1a92fql6mijhnr1kxkcxwivf95pk9lhgmhzkshs51h0ybfv5krik"))))
+   (properties `((upstream-name . "RcppNumerical")))
+   (build-system r-build-system)
+   (propagated-inputs
+    `(("r-rcpp" ,r-rcpp)
+      ("r-rcppeigen" ,r-rcppeigen)))
+   (native-inputs
+    `(("r-knitr" ,r-knitr)))
+   (home-page "https://github.com/yixuan/RcppNumerical")
+   (synopsis "Rcpp integration for numerical computing libraries")
+   (description "This package provides a collection of open source libraries
+for numerical computing (numerical integration, optimization, etc.) and their
+integration with @code{Rcpp}.")
+   (license license:gpl2+)))
+
+(define-public r-apeglm
+  (package
+   (name "r-apeglm")
+   (version "1.12.0")
+   (source (origin
+            (method url-fetch)
+            (uri (bioconductor-uri "apeglm" version))
+            (sha256
+             (base32
+              "0pix1fhxk2q89p2745fgsmxwics9rf10l392qhw3rw6v6ynhims2"))))
+   (properties `((upstream-name . "apeglm")))
+   (build-system r-build-system)
+   (propagated-inputs
+    `(("r-emdbook" ,r-emdbook)
+      ("r-genomicranges" ,r-genomicranges)
+      ("r-rcpp" ,r-rcpp)
+      ("r-rcppeigen" ,r-rcppeigen)
+      ("r-rcppnumerical" ,r-rcppnumerical)
+      ("r-summarizedexperiment" ,r-summarizedexperiment)))
+   (native-inputs `(("r-knitr" ,r-knitr)))
+   (home-page "https://bioconductor.org/packages/apeglm")
+   (synopsis "Approximate posterior estimation for GLM coefficients")
+   (description "This package provides Bayesian shrinkage estimators for
+effect sizes for a variety of GLM models, using approximation of the
+posterior for individual coefficients.")
+   (license license:gpl2)))
+
+(define-public r-greylistchip
+  (package
+   (name "r-greylistchip")
+   (version "1.22.0")
+   (source (origin
+            (method url-fetch)
+            (uri (bioconductor-uri "GreyListChIP" version))
+            (sha256
+             (base32
+              "1d1yvza1aw3vs3di6mrra5l52ig0p9bpzprrqvknjaz5i4yb8ma6"))))
+   (properties `((upstream-name . "GreyListChIP")))
+   (build-system r-build-system)
+   (propagated-inputs
+    `(("r-bsgenome" ,r-bsgenome)
+      ("r-genomeinfodb" ,r-genomeinfodb)
+      ("r-genomicalignments" ,r-genomicalignments)
+      ("r-genomicranges" ,r-genomicranges)
+      ("r-mass" ,r-mass)
+      ("r-rsamtools" ,r-rsamtools)
+      ("r-rtracklayer" ,r-rtracklayer)
+      ("r-summarizedexperiment" ,r-summarizedexperiment)))
+   (home-page "https://bioconductor.org/packages/GreyListChIP")
+   (synopsis "Greylist artefact regions based on ChIP inputs")
+   (description "This package identifies regions of ChIP experiments with high
+signal in the input, that lead to spurious peaks during peak calling.")
+   (license license:artistic2.0)))
+
 (define-public r-diffbind
   (package
     (name "r-diffbind")
-    (version "2.16.0")
+    (version "3.0.7")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DiffBind" version))
        (sha256
         (base32
-         "1mwqgljya1c7r2dfrdds3nswn9bn1l3ak1wavbpv4lbv3nkmykn5"))))
+         "0irhqsi6rrkrkc7dhwmfpqfd0mnigs17027czcx8vgbrbra4lcvd"))))
     (properties `((upstream-name . "DiffBind")))
     (build-system r-build-system)
     (inputs
      `(("zlib" ,zlib)))
     (propagated-inputs
      `(("r-amap" ,r-amap)
+       ("r-apeglm" ,r-apeglm)
+       ("r-ashr" ,r-ashr)
        ("r-biocparallel" ,r-biocparallel)
        ("r-deseq2" ,r-deseq2)
        ("r-dplyr" ,r-dplyr)
-       ("r-edger" ,r-edger)
        ("r-genomicalignments" ,r-genomicalignments)
        ("r-genomicranges" ,r-genomicranges)
        ("r-ggplot2" ,r-ggplot2)
        ("r-ggrepel" ,r-ggrepel)
        ("r-gplots" ,r-gplots)
+       ("r-greylistchip" ,r-greylistchip)
        ("r-iranges" ,r-iranges)
        ("r-lattice" ,r-lattice)
        ("r-limma" ,r-limma)
@@ -1687,14 +1767,14 @@ processing to visualization and annotation.")
 (define-public r-multtest
   (package
     (name "r-multtest")
-    (version "2.44.0")
+    (version "2.46.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "multtest" version))
        (sha256
         (base32
-         "12li7nzzygm3sjfx472095irqpawixk48d0k591wlnrms6sxchx2"))))
+         "06vixd81nh3nxrc6km73p7c4bwln1zm39fa9gp7gj272vsxkx53q"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-survival" ,r-survival)
@@ -1725,13 +1805,13 @@ expressed genes in DNA microarray experiments.")
 (define-public r-graph
   (package
     (name "r-graph")
-    (version "1.66.0")
+    (version "1.68.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "graph" version))
               (sha256
                (base32
-                "15v0nx9gzpszmdn5lil1s1y8qfmsirlznh56wcyqq4sxwjbyjn9g"))))
+                "0wr7j2pasvi3srvg9z3n034ljk8mldcixny6b3kmqbqm8dqy9py4"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)))
@@ -1765,6 +1845,32 @@ expressed genes in DNA microarray experiments.")
 fitting of some classes of graphical Markov models.")
     (license license:gpl2+)))
 
+;; This is a CRAN package, but it depends on a Bioconductor package, r-graph.
+(define-public r-perfmeas
+  (package
+    (name "r-perfmeas")
+    (version "1.2.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "PerfMeas" version))
+       (sha256
+        (base32
+         "1x7ancmb41zd1js24rx94plgbssyc71z2bvpic6mg34xjkwdjw93"))))
+    (properties `((upstream-name . "PerfMeas")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-graph" ,r-graph)
+       ("r-limma" ,r-limma)
+       ("r-rbgl" ,r-rbgl)))
+    (home-page "https://cran.r-project.org/web/packages/PerfMeas/")
+    (synopsis "Performance measures for ranking and classification tasks")
+    (description
+     "This package implements different performance measures for
+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+)))
+
 ;; This is a CRAN package, but it depends on a Bioconductor package.
 (define-public r-codedepends
   (package
@@ -1797,36 +1903,31 @@ determining dependencies between variables, code improvement suggestions.")
 (define-public r-chippeakanno
   (package
     (name "r-chippeakanno")
-    (version "3.22.4")
+    (version "3.24.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChIPpeakAnno" version))
        (sha256
         (base32
-         "0wxgjdikinkqj7jvs2725ak0291q6zhikyf1c93w8cngwvd9i1gq"))))
+         "0qdkwjv8s46d1kmgg2chijv7yzy9sv49kiks18w8x2z89prn15gj"))))
     (properties `((upstream-name . "ChIPpeakAnno")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-biobase" ,r-biobase)
        ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocmanager" ,r-biocmanager)
        ("r-biomart" ,r-biomart)
        ("r-biostrings" ,r-biostrings)
-       ("r-bsgenome" ,r-bsgenome)
        ("r-dbi" ,r-dbi)
-       ("r-delayedarray" ,r-delayedarray)
        ("r-ensembldb" ,r-ensembldb)
        ("r-genomeinfodb" ,r-genomeinfodb)
        ("r-genomicalignments" ,r-genomicalignments)
        ("r-genomicfeatures" ,r-genomicfeatures)
        ("r-genomicranges" ,r-genomicranges)
-       ("r-go-db" ,r-go-db)
+       ("r-ggplot2" ,r-ggplot2)
        ("r-graph" ,r-graph)
-       ("r-idr" ,r-idr)
        ("r-iranges" ,r-iranges)
-       ("r-limma" ,r-limma)
+       ("r-keggrest" ,r-keggrest)
        ("r-matrixstats" ,r-matrixstats)
        ("r-multtest" ,r-multtest)
        ("r-rbgl" ,r-rbgl)
@@ -1834,7 +1935,6 @@ determining dependencies between variables, code improvement suggestions.")
        ("r-rsamtools" ,r-rsamtools)
        ("r-rtracklayer" ,r-rtracklayer)
        ("r-s4vectors" ,r-s4vectors)
-       ("r-seqinr" ,r-seqinr)
        ("r-summarizedexperiment" ,r-summarizedexperiment)
        ("r-venndiagram" ,r-venndiagram)))
     (native-inputs
@@ -1855,12 +1955,12 @@ enrichedGO (addGeneIDs).")
 (define-public r-marray
   (package
     (name "r-marray")
-    (version "1.66.0")
+    (version "1.68.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "marray" version))
               (sha256
-               (base32 "1sym3nis5qzg05b2in83xr019mvz8czy8qvispc0hzsq42yng6kd"))))
+               (base32 "1kkgv166gzvlj8p58vzam3hcaz8mypi3hhpdsjhaszwg6nav4ray"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-limma" ,r-limma)))
@@ -1874,12 +1974,12 @@ normalization and quality checking.")
 (define-public r-cghbase
   (package
    (name "r-cghbase")
-   (version "1.48.0")
+   (version "1.50.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "CGHbase" version))
             (sha256
-             (base32 "0gfqqa9rs5hid53ihlky88qndgrwxxz0s6j7s505f660dd5nzlkf"))))
+             (base32 "10zhjmls3f63cj0bnywjb97zhrj7x3xsq6yjhvf5cclxc4kcrcx4"))))
    (properties `((upstream-name . "CGHbase")))
    (build-system r-build-system)
    (propagated-inputs
@@ -1894,12 +1994,12 @@ the @code{arrayCGH} packages.")
 (define-public r-cghcall
   (package
    (name "r-cghcall")
-   (version "2.50.0")
+   (version "2.52.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "CGHcall" version))
             (sha256
-             (base32 "1dz6sag8khl18vkb97b5w6fk6k9s7s9xxnc467dd3bmhmajlmrrg"))))
+             (base32 "1a6k87xfm79wnsc30k5aziakv51h4dd9zqw81q8bd72hc3fpz8ba"))))
    (properties `((upstream-name . "CGHcall")))
    (build-system r-build-system)
    (propagated-inputs
@@ -1917,12 +2017,12 @@ the @code{arrayCGH} packages.")
 (define-public r-qdnaseq
   (package
     (name "r-qdnaseq")
-    (version "1.24.0")
+    (version "1.26.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "QDNAseq" version))
               (sha256
-               (base32 "1ji9pl2r1idyj3qzggj7qd2kqx31i6b3igwk2hqjb8qzkyb37p86"))))
+               (base32 "1njka1ldaj12id3m2z8ghlrm2lg0n5pxsxyv5gpjnsiabnnaw6ph"))))
     (properties `((upstream-name . "QDNAseq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1950,14 +2050,14 @@ respectively.")
 (define-public r-bayseq
   (package
     (name "r-bayseq")
-    (version "2.22.0")
+    (version "2.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "baySeq" version))
        (sha256
         (base32
-         "1x0d34pqv9s15nmmxsfbw0ycxbf5348mi30ahycarjkjsyzycymj"))))
+         "1496inlw0x4mfy3g2v7j9ips96sf7576ydnfn6hvn2m6rz2ls215"))))
     (properties `((upstream-name . "baySeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2010,14 +2110,14 @@ datasets.")
 (define-public r-riboprofiling
   (package
     (name "r-riboprofiling")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RiboProfiling" version))
        (sha256
         (base32
-         "0s30m96dbbrzbywz3wai5ar0nsshb16lq101nyl20w1bk7sk2bha"))))
+         "112071w7aw7cwckipq0dll1lssl7pwafma4v9jj9sx12rjcj57xg"))))
     (properties `((upstream-name . "RiboProfiling")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2051,14 +2151,14 @@ assessment, principal component analysis on codon coverage.")
 (define-public r-riboseqr
   (package
     (name "r-riboseqr")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "riboSeqR" version))
        (sha256
         (base32
-         "04a4dkmacd6xy55m84amxa0fspbc4kgg9r9k7bc3wrxswk77ccxk"))))
+         "07i64gch14rsbjlfv17s689wzlqbi7hcqhcw21pp6cw8bvhvd5xr"))))
     (properties `((upstream-name . "riboSeqR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2154,14 +2254,14 @@ information and producing various plots and statistics.")
 (define-public r-ctc
   (package
     (name "r-ctc")
-    (version "1.62.0")
+    (version "1.64.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ctc" version))
        (sha256
         (base32
-         "0lv126xj092hps3f3dsv7hasdyy26wcx8npl9idq2l4h9addk6v6"))))
+         "1nwlphbfba3w8ixck02k5c84qm4flnp9fd68li0jn5a08qi9gmyp"))))
     (build-system r-build-system)
     (propagated-inputs `(("r-amap" ,r-amap)))
     (home-page "https://bioconductor.org/packages/ctc/")
@@ -2174,14 +2274,14 @@ trees and clusters to other programs.")
 (define-public r-goseq
   (package
     (name "r-goseq")
-    (version "1.40.0")
+    (version "1.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "goseq" version))
        (sha256
         (base32
-         "1iyri4rrchzsn8p6wjxr4k30d3cqx3km5mnd9hkfm5d0s7fjzlym"))))
+         "18fs3m4kl3zahn42j20rjvxy83irscgqx0dvid7va4majvsib509"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
@@ -2200,20 +2300,24 @@ defined categories which are over/under represented in RNA-seq data.")
 (define-public r-glimma
   (package
     (name "r-glimma")
-    (version "1.16.0")
+    (version "2.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Glimma" version))
        (sha256
         (base32
-         "1bxfgwjqb9p400a5a5q6p17kcnl3ddz090llihkfih9kyxii9n4y"))))
+         "0gy30v30lw27frhmw39pzacqzrv2vwj5rsp6gb3yifllrahdiffv"))))
     (properties `((upstream-name . "Glimma")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-edger" ,r-edger)
+     `(("r-deseq2" ,r-deseq2)
+       ("r-edger" ,r-edger)
+       ("r-htmlwidgets" ,r-htmlwidgets)
        ("r-jsonlite" ,r-jsonlite)
-       ("r-s4vectors" ,r-s4vectors)))
+       ("r-limma" ,r-limma)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)))
     (native-inputs
      `(("r-knitr" ,r-knitr)))
     (home-page "https://github.com/Shians/Glimma")
@@ -2229,14 +2333,14 @@ information.")
 (define-public r-rots
   (package
     (name "r-rots")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ROTS" version))
        (sha256
         (base32
-         "1mqhi1rfiw7mhiyify7vm3w17p7sc76wjda3ak6690hrc3gsm3cm"))))
+         "0qk0gfhgr14g13zlfyf5101b5s8cma7j3r8a92q93h0axy8ka23n"))))
     (properties `((upstream-name . "ROTS")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2253,14 +2357,14 @@ in omics data.")
 (define-public r-plgem
   (package
     (name "r-plgem")
-    (version "1.60.0")
+    (version "1.62.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "plgem" version))
        (sha256
         (base32
-         "1fs5nbjnrm7x23y7d9krq56r1kzxka40ca1rs6sq70mn6syhj90a"))))
+         "039gqwsm1v6q8v8b248nm8g9gnsk379mfx65rbgdmh3chsd8pm8a"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biobase" ,r-biobase)
@@ -2707,13 +2811,13 @@ gene and isoform level using RNA-seq data")
 (define-public r-karyoploter
   (package
     (name "r-karyoploter")
-    (version "1.14.0")
+    (version "1.14.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "karyoploteR" version))
               (sha256
                (base32
-                "0h0gk4xd95k5phy6qcsv7j931d7gk3p24i2fg4mz5dsk110lpifs"))))
+                "1wlnzkq58baqj9854nzf5rbglchb2xy4wsp3s0q8xfq8v0p3baxf"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
@@ -3628,14 +3732,14 @@ information about samples and features can be added to the plot.")
 (define-public r-gosemsim
   (package
     (name "r-gosemsim")
-    (version "2.14.1")
+    (version "2.14.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GOSemSim" version))
        (sha256
         (base32
-         "0v4q9xr1cm5xr08pgbzrss41kh3yz7xyh31n55l0sjmr1629ykln"))))
+         "02r7m1x6g8bb7q8l0hpvakdzdv5v1nplhx5lbiy798a7c3xg895b"))))
     (properties `((upstream-name . "GOSemSim")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4364,14 +4468,14 @@ position-specific scores within R and Bioconductor.")
 (define-public r-atacseqqc
   (package
     (name "r-atacseqqc")
-    (version "1.12.4")
+    (version "1.12.5")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ATACseqQC" version))
        (sha256
         (base32
-         "1gs9862hhh4gr1akij6ykhcj29s9dzg1vnj87hqrm19dfgl43qbh"))))
+         "1103daz82k97vzmxjmf7jwm2nd3w8i0jwplrsi9996bkih11qwbf"))))
     (properties `((upstream-name . "ATACseqQC")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5062,14 +5166,14 @@ based on @dfn{Continuous Wavelet Transform} (CWT).")
 (define-public r-xcms
   (package
     (name "r-xcms")
-    (version "3.10.1")
+    (version "3.10.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "xcms" version))
        (sha256
         (base32
-         "1aa11gy1v7kkamv3hsnvdx715q8f1saw9p664j6wifyjj0hx13kn"))))
+         "0sk53jcl7sjrpw2ncdpl8sw1b1j9mizlrj517rinr1qrbm6lsn8f"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biobase" ,r-biobase)
@@ -7247,14 +7351,14 @@ gene expression.")
 (define-public r-bgx
   (package
     (name "r-bgx")
-    (version "1.54.0")
+    (version "1.54.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bgx" version))
        (sha256
         (base32
-         "0r67a6m5hrnsxgk0f57hl5yaagi2wai2kpfyjjlhrck4rlm1sjcx"))))
+         "0a10fg9n5p024jrmbis102gqpbz23sc6vdn1sal2697hlxikzb46"))))
     (properties `((upstream-name . "bgx")))
     (build-system r-build-system)
     (propagated-inputs