gnu: r-gamlss: Update to 5.2-0.

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

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index fc9f171..a9f8ff2 100644 (file)
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3,6 +3,7 @@
 ;;; 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 © 2020 Peter Lo <peterloleungyau@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -798,14 +799,14 @@ closely reconstructs the mutational profile.")
 (define-public r-nmf
   (package
     (name "r-nmf")
-    (version "0.22.0")
+    (version "0.23.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "NMF" version))
        (sha256
         (base32
-         "0b2ls3x1nkrnam45hagpys624nzxj3v7kxnp0q216yakvx5h57cq"))))
+         "0ls7q9yc9l1z10jphq5a11wkfgcxc3gm3sfjj376zx3vnc0wl30g"))))
     (properties `((upstream-name . "NMF")))
     (build-system r-build-system)
     (propagated-inputs
@@ -826,6 +827,8 @@ closely reconstructs the mutational profile.")
        ("r-reshape2" ,r-reshape2)
        ("r-rngtools" ,r-rngtools)
        ("r-stringr" ,r-stringr)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "http://renozao.github.io/NMF")
     (synopsis "Algorithms and framework for nonnegative matrix factorization")
     (description
@@ -1396,14 +1399,14 @@ the Human Protein Atlas project.")
 (define-public r-regioner
   (package
     (name "r-regioner")
-    (version "1.20.0")
+    (version "1.20.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "regioneR" version))
        (sha256
         (base32
-         "10i21gxv0n7lrflhj5ja672xjizy1i4y4iq3pmjgbf0dpy1lxsih"))))
+         "0bzjwzj5mvb49wgvs3gd3jfpm7s0zfkca763i65i7m994lgvz33c"))))
     (properties `((upstream-name . "regioneR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1502,14 +1505,14 @@ browser.")
 (define-public r-oligoclasses
   (package
     (name "r-oligoclasses")
-    (version "1.50.0")
+    (version "1.50.4")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "oligoClasses" version))
        (sha256
         (base32
-         "05jy9qz3ir4maxackr1xqlfi1czhy1qd22wwibjdhfh5dp534cpn"))))
+         "1d8c3i8v8kcm1afgpz6zc1iysip7993y8456cqxl37f7n6n0ax67"))))
     (properties `((upstream-name . "oligoClasses")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1537,14 +1540,14 @@ packages.")
 (define-public r-oligo
   (package
     (name "r-oligo")
-    (version "1.52.0")
+    (version "1.52.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "oligo" version))
        (sha256
         (base32
-         "102szyiicws4c6l3k282236ml1m1vl9zmars4q1kdjfnvsyclfc4"))))
+         "1gpvr33pwzz1glzajcipvjcplb7yxvjj00q0ybqcc3wa47bhfkwd"))))
     (properties `((upstream-name . "oligo")))
     (build-system r-build-system)
     (inputs `(("zlib" ,zlib)))
@@ -1587,7 +1590,7 @@ Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
        ("r-reshape2" ,r-reshape2)))
     (native-inputs
      `(("r-knitr" ,r-knitr)))
-    (home-page "http://github.com/jdstorey/qvalue")
+    (home-page "https://github.com/StoreyLab/qvalue")
     (synopsis "Q-value estimation for false discovery rate control")
     (description
      "This package takes a list of p-values resulting from the simultaneous
@@ -1760,6 +1763,7 @@ 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.
 (define-public r-codedepends
   (package
     (name "r-codedepends")
@@ -1791,14 +1795,14 @@ determining dependencies between variables, code improvement suggestions.")
 (define-public r-chippeakanno
   (package
     (name "r-chippeakanno")
-    (version "3.22.2")
+    (version "3.22.3")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChIPpeakAnno" version))
        (sha256
         (base32
-         "199mlg0gwjy39afyk0ah6lzcm759bzxla4hgcajj0ay9jiibjqpa"))))
+         "0q3f55hh0a2hl96272js6gagmgps9cxs8s13pf6fii64rzaz5m7y"))))
     (properties `((upstream-name . "ChIPpeakAnno")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2934,7 +2938,7 @@ qPCR data, but could be used with other types as well.")
      (origin
        (method git-fetch)
        (uri (git-reference
-             (url "https://github.com/cole-trapnell-lab/monocle3.git")
+             (url "https://github.com/cole-trapnell-lab/monocle3")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
@@ -3450,14 +3454,14 @@ surface of a flowcell.")
 (define-public r-gkmsvm
   (package
     (name "r-gkmsvm")
-    (version "0.80.0")
+    (version "0.81.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "gkmSVM" version))
        (sha256
         (base32
-         "0ljcga246ad0ql8x3drvrdsyp0f20mgp3p6lnl79xb76qgfdnm0p"))))
+         "119g5rhc7ffyviz04r04aj5z1g6abnj3ddd01g7db505sdr6lapj"))))
     (properties `((upstream-name . "gkmSVM")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3622,14 +3626,14 @@ information about samples and features can be added to the plot.")
 (define-public r-gosemsim
   (package
     (name "r-gosemsim")
-    (version "2.14.0")
+    (version "2.14.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GOSemSim" version))
        (sha256
         (base32
-         "0mg4d8whq90iyl2jjj5dx3kyar17yqn00jvia3b4a8lhmjw8l1hk"))))
+         "0v4q9xr1cm5xr08pgbzrss41kh3yz7xyh31n55l0sjmr1629ykln"))))
     (properties `((upstream-name . "GOSemSim")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3810,14 +3814,14 @@ All the visualization methods are developed based on ggplot2 graphics.")
 (define-public r-clusterprofiler
   (package
     (name "r-clusterprofiler")
-    (version "3.16.0")
+    (version "3.16.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "clusterProfiler" version))
        (sha256
         (base32
-         "0m7919gzrd2fddb4kcznwpshhab1ha2yppnkxg11zmh40wcdawyi"))))
+         "11zsgb8wbdv8r4c04iczz4aala4yw4ai7rz8igdzz87c0940nxkb"))))
     (properties
      `((upstream-name . "clusterProfiler")))
     (build-system r-build-system)
@@ -3832,6 +3836,7 @@ All the visualization methods are developed based on ggplot2 graphics.")
        ("r-magrittr" ,r-magrittr)
        ("r-plyr" ,r-plyr)
        ("r-qvalue" ,r-qvalue)
+       ("r-rlang" ,r-rlang)
        ("r-rvcheck" ,r-rvcheck)
        ("r-tidyr" ,r-tidyr)))
     (native-inputs
@@ -4087,7 +4092,8 @@ Affymetrix arrays.")
     (properties `((upstream-name . "abseqR")))
     (build-system r-build-system)
     (inputs
-     `(("pandoc" ,ghc-pandoc)))
+     `(("pandoc" ,pandoc)
+       ("pandoc-citeproc" ,pandoc-citeproc)))
     (propagated-inputs
      `(("r-biocparallel" ,r-biocparallel)
        ("r-biocstyle" ,r-biocstyle)
@@ -4287,14 +4293,14 @@ Bioconductor.")
 (define-public r-motifstack
   (package
     (name "r-motifstack")
-    (version "1.32.0")
+    (version "1.32.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "motifStack" version))
        (sha256
         (base32
-         "008f2mjcyyiz84ilrsldpqwvxy2lp93hjggrq4nrqwi78nyx3ls5"))))
+         "02vmkgn36n5xpmizy33znlzgmi3w5hnhsibgisbnhwwgxpkrwpcd"))))
     (properties `((upstream-name . "motifStack")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4356,14 +4362,14 @@ position-specific scores within R and Bioconductor.")
 (define-public r-atacseqqc
   (package
     (name "r-atacseqqc")
-    (version "1.12.3")
+    (version "1.12.4")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ATACseqQC" version))
        (sha256
         (base32
-         "12710c4024pndwwqiiqr6dhrd360z26fc8r3fxhs739gyd0ddk9r"))))
+         "1gs9862hhh4gr1akij6ykhcj29s9dzg1vnj87hqrm19dfgl43qbh"))))
     (properties `((upstream-name . "ATACseqQC")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5119,14 +5125,14 @@ that arising from 16s metagenomic surveys.")
 (define-public r-wiggleplotr
   (package
     (name "r-wiggleplotr")
-    (version "1.12.0")
+    (version "1.12.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "wiggleplotr" version))
        (sha256
         (base32
-         "15l8f7ls2mwhsw68sr1k4r19hmdzjriibr5hpnfbanzj5x6yhdjq"))))
+         "1wknigh1md3w4h68caqlpq945maipdkpmw10hc2rlx4nbbpcnawp"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-assertthat" ,r-assertthat)
@@ -5236,14 +5242,14 @@ This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
 (define-public r-rbowtie2
   (package
     (name "r-rbowtie2")
-    (version "1.10.0")
+    (version "1.10.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rbowtie2" version))
        (sha256
         (base32
-         "1z2dn0q3wcw8b9ibx388kh7p5km16i71sw9miqj3daw7g0v5bxp3"))))
+         "19v7wfvrd53j618c1xbiqnlsf2kxw697myryx0vb9s2aspknyzz7"))))
     (properties `((upstream-name . "Rbowtie2")))
     (build-system r-build-system)
     (inputs
@@ -5314,14 +5320,14 @@ Infinium HumanMethylation 450k assay.")
 (define-public r-biocfilecache
   (package
     (name "r-biocfilecache")
-    (version "1.12.0")
+    (version "1.12.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocFileCache" version))
        (sha256
         (base32
-         "02chrzwccmazi7rdfpyriizhbgxyxlmprlw32w05wk54as6wrxv8"))))
+         "02yayjyliaqxcwqa0n2ccmsfflskqzf0gvdibh2r3nz5bi66imkf"))))
     (properties `((upstream-name . "BiocFileCache")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5376,14 +5382,14 @@ Gaussian distributions.")
 (define-public r-rbowtie
   (package
     (name "r-rbowtie")
-    (version "1.28.0")
+    (version "1.28.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rbowtie" version))
        (sha256
         (base32
-         "06y1qp915dlwjdi2fs3344sgya55pcv07f3i61y0cxb0bhbcgvrz"))))
+         "0589ggbfx6di42wvqyhnzgrhmb52swr3r5z22w6b8x0z2y7hl8b3"))))
     (properties `((upstream-name . "Rbowtie")))
     (build-system r-build-system)
     (inputs
@@ -5781,14 +5787,14 @@ annotations.")
 (define-public r-rsubread
   (package
     (name "r-rsubread")
-    (version "2.2.2")
+    (version "2.2.6")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rsubread" version))
        (sha256
         (base32
-         "1wgilpaw70dwg0zilx5i1pmi4j8wri6wi2ha1d3bapfhlwc6igml"))))
+         "04h79qhq93d8id0rr5xnj9vf82ygwxzdlnck78yv738xd0jjvnpm"))))
     (properties `((upstream-name . "Rsubread")))
     (build-system r-build-system)
     (inputs `(("zlib" ,zlib)))
@@ -6087,14 +6093,14 @@ model with Box-Cox transformation.")
 (define-public r-rprotobuflib
   (package
     (name "r-rprotobuflib")
-    (version "1.8.0")
+    (version "2.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RProtoBufLib" version))
        (sha256
         (base32
-         "0dlgki21a37bxqh3cf83vl5zqxm86472g8a9plvhrjzzsn3mwnrm"))))
+         "0kfinf9vzc1i5qxmaw832id557gr1vqdi1m8yiaxz83g37wh8vps"))))
     (properties `((upstream-name . "RProtoBufLib")))
     (build-system r-build-system)
     (arguments
@@ -6103,8 +6109,10 @@ model with Box-Cox transformation.")
          (add-after 'unpack 'unpack-bundled-sources
            (lambda _
              (with-directory-excursion "src"
-               (invoke "tar" "xf" "protobuf-2.6.0.tgz"))
+               (invoke "tar" "xf" "protobuf-3.10.0.tar.gz"))
              #t)))))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://bioconductor.org/packages/RProtoBufLib/")
     (synopsis "C++ headers and static libraries of Protocol buffers")
     (description
@@ -6115,14 +6123,14 @@ for other R packages to compile and link against.")
 (define-public r-flowworkspace
   (package
     (name "r-flowworkspace")
-    (version "3.34.1")
+    (version "4.0.6")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowWorkspace" version))
        (sha256
         (base32
-         "1ijbc6z9ljhrw3cqr02smgplhrfg44gzrb1dq4gbrpq3nj4khhpn"))))
+         "123ny8n3jjgmsnpghk1dafxkwmcyr513gxi8y4h4qszq4s6ai15v"))))
     (properties `((upstream-name . "flowWorkspace")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6134,21 +6142,24 @@ for other R packages to compile and link against.")
        ("r-digest" ,r-digest)
        ("r-dplyr" ,r-dplyr)
        ("r-flowcore" ,r-flowcore)
-       ("r-flowviz" ,r-flowviz)
+       ("r-ggplot2" ,r-ggplot2)
        ("r-graph" ,r-graph)
-       ("r-gridextra" ,r-gridextra)
        ("r-lattice" ,r-lattice)
        ("r-latticeextra" ,r-latticeextra)
        ("r-matrixstats" ,r-matrixstats)
        ("r-ncdfflow" ,r-ncdfflow)
        ("r-rbgl" ,r-rbgl)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)
        ("r-rcpp" ,r-rcpp)
+       ("r-rcpparmadillo" ,r-rcpparmadillo)
        ("r-rcppparallel" ,r-rcppparallel)
        ("r-rgraphviz" ,r-rgraphviz)
+       ("r-rhdf5lib" ,r-rhdf5lib)
        ("r-rprotobuflib" ,r-rprotobuflib)
        ("r-scales" ,r-scales)
-       ("r-stringr" ,r-stringr)))
+       ("r-stringr" ,r-stringr)
+       ("r-xml" ,r-xml)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://bioconductor.org/packages/flowWorkspace/")
     (synopsis "Infrastructure for working with cytometry data")
     (description
@@ -6163,14 +6174,14 @@ matches the flowJo analysis.")
 (define-public r-flowstats
   (package
     (name "r-flowstats")
-    (version "3.44.0")
+    (version "4.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowStats" version))
        (sha256
         (base32
-         "0pql0lpf90nra7w6z6nd8l9cgjlsg2pxysfravnbzfhl3pjvd96w"))))
+         "1ygvxvd7y6jp907y0h3hycdwvw1fch16w84g06nk4f4g4kvrzdir"))))
     (properties `((upstream-name . "flowStats")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6199,14 +6210,14 @@ package.")
 (define-public r-opencyto
   (package
     (name "r-opencyto")
-    (version "1.24.0")
+    (version "2.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "openCyto" version))
        (sha256
         (base32
-         "0h25nhvq1zq624wsgb55wjcgri9rcd2fnqkb31h9jdakr01dw2sb"))))
+         "10dyd6dddskv70vhpwfbsqdb8pb9i3ka0fgvl1h51wqlckbsj89m"))))
     (properties `((upstream-name . "openCyto")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6231,6 +6242,8 @@ package.")
        ("r-rcolorbrewer" ,r-rcolorbrewer)
        ("r-rcpp" ,r-rcpp)
        ("r-rrcov" ,r-rrcov)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://bioconductor.org/packages/openCyto")
     (synopsis "Hierarchical gating pipeline for flow cytometry data")
     (description
@@ -6241,14 +6254,14 @@ sequential way to mimic the manual gating strategy.")
 (define-public r-cytoml
   (package
     (name "r-cytoml")
-    (version "1.12.1")
+    (version "2.0.5")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "CytoML" version))
        (sha256
         (base32
-         "0wgi8rwb4spxzd5xvs5amfr5g82ny2nad57j3nmhnhnj1cpirjxz"))))
+         "174brv027mm90lydfg6hnhazwh8jy4vf6ial4hpsfalwa5jrz55n"))))
     (properties `((upstream-name . "CytoML")))
     (build-system r-build-system)
     (inputs
@@ -6267,16 +6280,19 @@ sequential way to mimic the manual gating strategy.")
        ("r-graph" ,r-graph)
        ("r-jsonlite" ,r-jsonlite)
        ("r-lattice" ,r-lattice)
-       ("r-ncdfflow" ,r-ncdfflow)
        ("r-opencyto" ,r-opencyto)
        ("r-plyr" ,r-plyr)
        ("r-rbgl" ,r-rbgl)
        ("r-rcpp" ,r-rcpp)
+       ("r-rcpparmadillo" ,r-rcpparmadillo)
        ("r-rcppparallel" ,r-rcppparallel)
        ("r-rgraphviz" ,r-rgraphviz)
+       ("r-rhdf5lib" ,r-rhdf5lib)
        ("r-rprotobuflib" ,r-rprotobuflib)
        ("r-runit" ,r-runit)
+       ("r-tibble" ,r-tibble)
        ("r-xml" ,r-xml)
+       ("r-xml2" ,r-xml2)
        ("r-yaml" ,r-yaml)))
     (native-inputs
      `(("r-knitr" ,r-knitr)))
@@ -6290,14 +6306,14 @@ standard to exchange gated cytometry data with other software platforms.")
 (define-public r-flowsom
   (package
     (name "r-flowsom")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "FlowSOM" version))
        (sha256
         (base32
-         "0265sq4zvj6d6h5ghqj9xzm4b0z9v65kgyl88cgdcpdkzfnfcvd5"))))
+         "1p17jv4q1dbcc47jpjy9hbcvzpwrx8waq7qpcj778jsyz6z6jh78"))))
     (properties `((upstream-name . "FlowSOM")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6320,14 +6336,14 @@ self-organizing map clustering and minimal spanning trees.")
 (define-public r-mixomics
   (package
     (name "r-mixomics")
-    (version "6.10.9")
+    (version "6.12.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "mixOmics" version))
        (sha256
         (base32
-         "0b457yg8mwqlrn5l344w8qcj8v2ghlj1wdx1ysxbncqvqx7nvgig"))))
+         "1nkqlvm9j1f4vfj3f3kyxqgan38rpa9imimvl9pwivvsfl647vvc"))))
     (properties `((upstream-name . "mixOmics")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6364,14 +6380,14 @@ delete entire rows with missing data.")
 (define-public r-depecher
   (package
     (name "r-depecher")
-    (version "1.2.2")
+    (version "1.4.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DepecheR" version))
        (sha256
         (base32
-         "199j2kw0xnw7y4v1gakm2jgyc7zzlj8xh0570f2yjq55gp1kggbm"))))
+         "0dscfl6wxpl5538jzkrwisdwbr873d38rzd19vl6z5br71jvpv3v"))))
     (properties `((upstream-name . "DepecheR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6409,14 +6425,14 @@ data, to only emphasize the data that actually matters.")
 (define-public r-rcistarget
   (package
     (name "r-rcistarget")
-    (version "1.6.0")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RcisTarget" version))
        (sha256
         (base32
-         "1nnah7s0jd24fpfyxsf76jas8dm23c3266aps124wdlqsp9q5qjw"))))
+         "1lvi873dv0vhw53s1pmcilw8qwlywm9p2ybphcl168nzh6w31r4i"))))
     (properties `((upstream-name . "RcisTarget")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6427,6 +6443,8 @@ data, to only emphasize the data that actually matters.")
        ("r-gseabase" ,r-gseabase)
        ("r-r-utils" ,r-r-utils)
        ("r-summarizedexperiment" ,r-summarizedexperiment)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://aertslab.org/#scenic")
     (synopsis "Identify transcription factor binding motifs enriched on a gene list")
     (description
@@ -6444,14 +6462,14 @@ genes in the gene-set that are ranked above the leading edge).")
 (define-public r-cicero
   (package
     (name "r-cicero")
-    (version "1.4.4")
+    (version "1.6.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "cicero" version))
        (sha256
         (base32
-         "1ay1g2r0la4grcp1y8vcp211lfwzjf7j819ajzdirsh5dab8whld"))))
+         "042ba6yfa7fksij2v7cwnp2sca3vmz7izn6fsxx9xswnncrkgcqh"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-assertthat" ,r-assertthat)
@@ -6471,6 +6489,7 @@ genes in the gene-set that are ranked above the leading edge).")
        ("r-plyr" ,r-plyr)
        ("r-reshape2" ,r-reshape2)
        ("r-s4vectors" ,r-s4vectors)
+       ("r-stringi" ,r-stringi)
        ("r-stringr" ,r-stringr)
        ("r-tibble" ,r-tibble)
        ("r-tidyr" ,r-tidyr)
@@ -6496,7 +6515,7 @@ accessibility data.")
        (origin
          (method git-fetch)
          (uri (git-reference
-               (url "https://github.com/cole-trapnell-lab/cicero-release.git")
+               (url "https://github.com/cole-trapnell-lab/cicero-release")
                (commit commit)))
          (file-name (git-file-name name version))
          (sha256
@@ -6517,7 +6536,7 @@ accessibility data.")
        (origin
          (method git-fetch)
          (uri (git-reference
-               (url "https://github.com/aertslab/cisTopic.git")
+               (url "https://github.com/aertslab/cisTopic")
                (commit commit)))
          (file-name (git-file-name name version))
          (sha256
@@ -6554,17 +6573,19 @@ cisTopics and explore the nature and regulatory proteins driving them.")
 (define-public r-genie3
   (package
     (name "r-genie3")
-    (version "1.8.0")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GENIE3" version))
        (sha256
         (base32
-         "0p67lhgy3lb4nc958s51hx7rvgwhzwfic9xhpsrask40k43spv7l"))))
+         "1bsm0gxracsyg1wnaw3whvskghfpbgbm9navr8wdmxj2hjp3dqs7"))))
     (properties `((upstream-name . "GENIE3")))
     (build-system r-build-system)
     (propagated-inputs `(("r-reshape2" ,r-reshape2)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://bioconductor.org/packages/GENIE3")
     (synopsis "Gene network inference with ensemble of trees")
     (description
@@ -6575,14 +6596,14 @@ regulatory networks from expression data.")
 (define-public r-roc
   (package
     (name "r-roc")
-    (version "1.62.0")
+    (version "1.64.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ROC" version))
        (sha256
         (base32
-         "1aqpyc28czagg3nbybh55vf152nbar61jjw79w04326d97mc3j3y"))))
+         "0gmx3r77yl5fqrj5j2hamwynbis75qd62q28964kx16z33xfgx89"))))
     (properties `((upstream-name . "ROC")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6623,14 +6644,14 @@ data.")
 (define-public r-watermelon
   (package
     (name "r-watermelon")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "wateRmelon" version))
        (sha256
         (base32
-         "0a66fq04yph9dis91lzjk9kh134zy6fj98yklrwf24r1080qngx0"))))
+         "1c3a6bq3ggmv8kmdfrgiar6nwgircgzjrbgd9z9dqiin7j13gxwn"))))
     (properties `((upstream-name . "wateRmelon")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6660,14 +6681,14 @@ metrics, with methods for objects produced by the @code{methylumi} and
 (define-public r-gdsfmt
   (package
     (name "r-gdsfmt")
-    (version "1.22.0")
+    (version "1.24.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gdsfmt" version))
        (sha256
         (base32
-         "0zc9v62imd0ykz4h30pxa64q0y45qijmkwdk2pd4ncsg8fc2jlz9"))
+         "0ipf60wylbhvwk9q3mbnak0f1n6k7spfh90s1c1c0b47ryxsri67"))
        (modules '((guix build utils)))
        ;; Remove bundled sources of zlib, lz4, and xz.  Don't attempt to build
        ;; them and link with system libraries instead.
@@ -6697,6 +6718,8 @@ metrics, with methods for objects produced by the @code{methylumi} and
      `(("lz4" ,lz4)
        ("xz" ,xz)
        ("zlib" ,zlib)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "http://corearray.sourceforge.net/")
     (synopsis
      "R Interface to CoreArray Genomic Data Structure (GDS) Files")
@@ -6717,14 +6740,14 @@ with multiple R processes supported by the package @code{parallel}.")
 (define-public r-bigmelon
   (package
     (name "r-bigmelon")
-    (version "1.12.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bigmelon" version))
        (sha256
         (base32
-         "0sw7rp4p03m1s72b4j06jfb7as3v1n2w2z4ppk8s4f80fb05bcls"))))
+         "1cryjhbiacm45g097rpqgbva49hs5vdx4y4h5h2v1gw4k78hwb4y"))))
     (properties `((upstream-name . "bigmelon")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6745,14 +6768,14 @@ with multiple R processes supported by the package @code{parallel}.")
 (define-public r-seqbias
   (package
     (name "r-seqbias")
-    (version "1.34.0")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "seqbias" version))
        (sha256
         (base32
-         "19vbdyjblij2533ibmrw1n0rkqfrbflma6cg5b79ghks0mg7z8hq"))))
+         "0sy2fv98x4qfz9llns28jh1n4bi991jj856y8a5fbzpx7y990lai"))))
     (properties `((upstream-name . "seqbias")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6811,14 +6834,14 @@ injected in that sequence).")
 (define-public r-reqon
   (package
     (name "r-reqon")
-    (version "1.32.0")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ReQON" version))
        (sha256
         (base32
-         "10p6l2zxijqyypdm970jyfqyrnfhaq3nf7cg2q6mgd1srggfa0cx"))))
+         "06m0hd4aqsxjyzhs8b1zys7lz8289qgwn7jp2dpln1j7cf02q4bz"))))
     (properties `((upstream-name . "ReQON")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6836,14 +6859,14 @@ format.")
 (define-public r-wavcluster
   (package
     (name "r-wavcluster")
-    (version "2.20.0")
+    (version "2.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "wavClusteR" version))
        (sha256
         (base32
-         "0vq3xxsvwq86rlya7xc92sc4i6b48sib0pcina3xivg3ky2j3z7y"))))
+         "0204czqjmkwhd6gznwxzb0vj3dg3aif628g8c30085aa2jljn9bk"))))
     (properties `((upstream-name . "wavClusteR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6862,6 +6885,8 @@ format.")
        ("r-seqinr" ,r-seqinr)
        ("r-stringr" ,r-stringr)
        ("r-wmtsa" ,r-wmtsa)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://bioconductor.org/packages/wavClusteR/")
     (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data")
     (description
@@ -6882,14 +6907,14 @@ procedures that induce nucleotide substitutions (e.g. BisSeq).")
 (define-public r-timeseriesexperiment
   (package
     (name "r-timeseriesexperiment")
-    (version "1.4.0")
+    (version "1.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "TimeSeriesExperiment" version))
        (sha256
         (base32
-         "0xqa6hzknnci20zx2f6mw5cpqx8pq0v6fzf053hh51p1l2ikvgqm"))))
+         "1k0djvcsyjj1ayncvmi8nlqi3jdn5qp41y3fwsqg1cp0qsvx7zv3"))))
     (properties
      `((upstream-name . "TimeSeriesExperiment")))
     (build-system r-build-system)
@@ -6909,6 +6934,8 @@ procedures that induce nucleotide substitutions (e.g. BisSeq).")
        ("r-tidyr" ,r-tidyr)
        ("r-vegan" ,r-vegan)
        ("r-viridis" ,r-viridis)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://github.com/nlhuong/TimeSeriesExperiment/")
     (synopsis "Analysis for short time-series data")
     (description
@@ -6921,14 +6948,14 @@ provides methods for retrieving enriched pathways.")
 (define-public r-variantfiltering
   (package
     (name "r-variantfiltering")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "VariantFiltering" version))
        (sha256
         (base32
-         "13pgfk2mbffd9smmxnwz7g0jrwng78711053wfzadr107zbyn4r8"))))
+         "0lsrnybsbm9siyjv4nal6bmprj8ynwgk4n1145f4h52g78wq3br4"))))
     (properties
      `((upstream-name . "VariantFiltering")))
     (build-system r-build-system)
@@ -7027,14 +7054,14 @@ arrays based on fast wavelet-based functional models.")
 (define-public r-variancepartition
   (package
     (name "r-variancepartition")
-    (version "1.16.1")
+    (version "1.18.3")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "variancePartition" version))
        (sha256
         (base32
-         "02pzsff14j4am2d949mh8xgi0c7k44g09q4lr6nqm08vf92brb6g"))))
+         "1jrlhi2c5ibvq8a41g5hwdq4kk4rdd7m464rz5767zaaci7l2ay0"))))
     (properties
      `((upstream-name . "variancePartition")))
     (build-system r-build-system)
@@ -7055,6 +7082,8 @@ arrays based on fast wavelet-based functional models.")
        ("r-progress" ,r-progress)
        ("r-reshape2" ,r-reshape2)
        ("r-scales" ,r-scales)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://bioconductor.org/packages/variancePartition/")
     (synopsis "Analyze variation in gene expression experiments")
     (description
@@ -7069,14 +7098,14 @@ measures.")
 (define-public r-htqpcr
   (package
     (name "r-htqpcr")
-    (version "1.40.0")
+    (version "1.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "HTqPCR" version))
        (sha256
         (base32
-         "008iczqaa0wn5nw144vfg3qylg7qa1q963nq9mqhgj3sxlg4rmjx"))))
+         "08bd5zkjdnz726s03bvvzv03va0xbrr818ipp6737z9g3nk9m81j"))))
     (properties `((upstream-name . "HTqPCR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7103,14 +7132,14 @@ features (e.g.  genes, microRNAs).")
 (define-public r-unifiedwmwqpcr
   (package
     (name "r-unifiedwmwqpcr")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "unifiedWMWqPCR" version))
        (sha256
         (base32
-         "1l6rf7scxxyz4x0m4li54y6905sqj4jrx481zb9h3vqhcfcmn8lj"))))
+         "1l9gxq3askr3cz2a4bqsw7vjr1agivzvx651cblkygv57x08zf81"))))
     (properties
      `((upstream-name . "unifiedWMWqPCR")))
     (build-system r-build-system)
@@ -7130,14 +7159,14 @@ data.")
 (define-public r-activedriverwgs
   (package
     (name "r-activedriverwgs")
-    (version "1.0.1")
+    (version "1.1.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ActiveDriverWGS" version))
        (sha256
         (base32
-         "08l9dj8d3cd74z1dqn8n4yqykwvqjxsfa067wnxyh7xnfvvnm5v1"))))
+         "0l6h0f54zjvcx19ngq3kp01dypsjqf28vssjm8yzccmpyacfypag"))))
     (properties
      `((upstream-name . "ActiveDriverWGS")))
     (build-system r-build-system)
@@ -7148,8 +7177,9 @@ data.")
        ("r-genomeinfodb" ,r-genomeinfodb)
        ("r-genomicranges" ,r-genomicranges)
        ("r-iranges" ,r-iranges)
-       ("r-plyr" ,r-plyr)
        ("r-s4vectors" ,r-s4vectors)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/")
     (synopsis "Driver discovery tool for cancer whole genomes")
     (description
@@ -7164,21 +7194,20 @@ using whole genome sequencing data.")
 (define-public r-activepathways
   (package
     (name "r-activepathways")
-    (version "1.0.1")
+    (version "1.0.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ActivePathways" version))
        (sha256
         (base32
-         "1xb0d1svmzw404pv8ja6wr4773k7x2lxkrzrayilvzqbfzj1wx20"))))
+         "1hxy760x141ykrpqdbfldq4ggj1svj3lsrpwi4rb2x7r4lna937l"))))
     (properties
      `((upstream-name . "ActivePathways")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-data-table" ,r-data-table)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-metap" ,r-metap)))
+       ("r-ggplot2" ,r-ggplot2)))
     (native-inputs
      `(("r-knitr" ,r-knitr)))
     (home-page "https://cran.r-project.org/web/packages/ActivePathways/")
@@ -7194,14 +7223,14 @@ cellular organization in health and disease.")
 (define-public r-bgmix
   (package
     (name "r-bgmix")
-    (version "1.46.0")
+    (version "1.48.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BGmix" version))
        (sha256
         (base32
-         "1bwqqhkh4m3hhpd71grwjrg7n07lzvys4y7aghmw2gw5ibnk5683"))))
+         "1pfi3hinjn6ymikadgj8dqm59h7mapf01wj86dbbvf8y1xqp8y8n"))))
     (properties `((upstream-name . "BGmix")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7216,14 +7245,14 @@ gene expression.")
 (define-public r-bgx
   (package
     (name "r-bgx")
-    (version "1.52.0")
+    (version "1.54.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bgx" version))
        (sha256
         (base32
-         "0fiqqv6pin0zhxaw67hzfjccq2qkl9qfqjf10nx2zmpxm2licavm"))))
+         "0r67a6m5hrnsxgk0f57hl5yaagi2wai2kpfyjjlhrck4rlm1sjcx"))))
     (properties `((upstream-name . "bgx")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7241,14 +7270,14 @@ Affymetrix GeneChips.")
 (define-public r-bhc
   (package
     (name "r-bhc")
-    (version "1.38.0")
+    (version "1.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BHC" version))
        (sha256
         (base32
-         "1bxx3jak8mgvay3j1xd59bb9j86pzl6hh5abxww9x1b7rswmy1jh"))))
+         "06milqjg2nl3ra47sxi7a2p2d3mbrx3wk168pqgimvs8snldd2xr"))))
     (properties `((upstream-name . "BHC")))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/BHC/")
@@ -7267,14 +7296,14 @@ algorithm which is more efficient for larger data sets.")
 (define-public r-bicare
   (package
     (name "r-bicare")
-    (version "1.44.0")
+    (version "1.46.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BicARE" version))
        (sha256
         (base32
-         "1gia5vzmvbk4k1vx3bh9nld1ws9s3c0y11qfbzqhfnfjbd7n8qcs"))))
+         "0llckbl3l26lf6wgjg7rxs8k1yrk043vvdhnkc6ncg33sydj383y"))))
     (properties `((upstream-name . "BicARE")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7291,19 +7320,21 @@ results.")
 (define-public r-bifet
   (package
     (name "r-bifet")
-    (version "1.6.0")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiFET" version))
        (sha256
         (base32
-         "0ck1d6hxd4f40hfz8p2z5xmjbz79yhrf6fisjka2xzk5v9fm4p4k"))))
+         "1v2dshs09iy2glzq0vwxmr83x867j844i1ixsfcamvfq33fwbbr5"))))
     (properties `((upstream-name . "BiFET")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-genomicranges" ,r-genomicranges)
        ("r-poibin" ,r-poibin)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://bioconductor.org/packages/BiFET")
     (synopsis "Bias-free footprint enrichment test")
     (description
@@ -7319,14 +7350,14 @@ the read count and GC content bias.")
 (define-public r-rsbml
   (package
     (name "r-rsbml")
-    (version "2.44.0")
+    (version "2.46.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "rsbml" version))
        (sha256
         (base32
-         "1dbp0aaijxn3na26b68ws0v9qzvml61ifb9z4i8pz7q6h48n7lxa"))))
+         "1i1izznnwzrc6m7s3hblfff466icfvxl2gjdqaln8qfg9v87rslx"))))
     (properties `((upstream-name . "rsbml")))
     (build-system r-build-system)
     (inputs
@@ -7347,14 +7378,14 @@ validating output, provides an S4 SBML DOM, converts SBML to R graph objects.")
 (define-public r-hypergraph
   (package
     (name "r-hypergraph")
-    (version "1.58.0")
+    (version "1.60.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "hypergraph" version))
        (sha256
         (base32
-         "1bixmslxy7r987zw1vf4dg72hfi04lf4vj03n7ygym2g8nfhbh7m"))))
+         "1iq9b9rzy3ikx8xszsjiv3p8l702n2h2s9w33797wcmkg4apslb7"))))
     (properties `((upstream-name . "hypergraph")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7369,14 +7400,14 @@ manipulating hypergraphs.")
 (define-public r-hyperdraw
   (package
     (name "r-hyperdraw")
-    (version "1.38.0")
+    (version "1.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "hyperdraw" version))
        (sha256
         (base32
-         "0a8h3pb7196qi49ady8ni92m5wqb1hvxw6khk9j63mwj3h7jinbj"))))
+         "1qzx5sqp7rpspk8g1j34p03ds1vmw0h7hpzb2ijpbvmsja5drzvf"))))
     (properties `((upstream-name . "hyperdraw")))
     (build-system r-build-system)
     (inputs `(("graphviz" ,graphviz)))
@@ -7393,14 +7424,14 @@ manipulating hypergraphs.")
 (define-public r-biggr
   (package
     (name "r-biggr")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiGGR" version))
        (sha256
         (base32
-         "1n2ypc84abmhn6br0yi87k7lvjc11k7abzhgvzdabc2ai1qgcqif"))))
+         "05afi6hsh1dv6lc6l0dfhvvi8k34wyzf1k1jimam7a6pbrhyy5dk"))))
     (properties `((upstream-name . "BiGGR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7423,19 +7454,21 @@ networks and estimated fluxes can be visualized with hypergraphs.")
 (define-public r-bigmemoryextras
   (package
     (name "r-bigmemoryextras")
-    (version "1.34.0")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bigmemoryExtras" version))
        (sha256
         (base32
-         "17dk7c44ikphcrpi8hnxyvlmj30qmj098kc0ihfi69bp9rw1cibq"))))
+         "053bqcd3p4i7agj43ccjxfz40a1sxrymd49vdpfq8ypslkwk7g0g"))))
     (properties
      `((upstream-name . "bigmemoryExtras")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-bigmemory" ,r-bigmemory)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://github.com/phaverty/bigmemoryExtras")
     (synopsis "Extension of the bigmemory package")
     (description
@@ -7455,18 +7488,19 @@ a file-backed matrix with factor properties.")
 (define-public r-bigpint
   (package
     (name "r-bigpint")
-    (version "1.2.2")
+    (version "1.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bigPint" version))
        (sha256
         (base32
-         "1zkakxi1iqavzmjxnkkd02qm5jk28ldcvcdcxaafz748dz6s67fs"))))
+         "1m92ngkzimcc37byf0ziphrby8wmjd5hfa53gvfphgaakyj9bjg8"))))
     (properties `((upstream-name . "bigPint")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-dplyr" ,r-dplyr)
+     `(("r-delayedarray" ,r-delayedarray)
+       ("r-dplyr" ,r-dplyr)
        ("r-ggally" ,r-ggally)
        ("r-ggplot2" ,r-ggplot2)
        ("r-gridextra" ,r-gridextra)
@@ -7481,6 +7515,7 @@ a file-backed matrix with factor properties.")
        ("r-shinycssloaders" ,r-shinycssloaders)
        ("r-shinydashboard" ,r-shinydashboard)
        ("r-stringr" ,r-stringr)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)
        ("r-tidyr" ,r-tidyr)))
     (native-inputs
      `(("r-knitr" ,r-knitr)))
@@ -7496,14 +7531,14 @@ visualizing RNA-sequencing datasets and differentially expressed genes.")
 (define-public r-chemminer
   (package
     (name "r-chemminer")
-    (version "3.38.0")
+    (version "3.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChemmineR" version))
        (sha256
         (base32
-         "1j6vmkhc03dmmkm5wgbcv62pw5dclp49f906xkx1pwg27bdldbga"))))
+         "0cna5xsqflvhlp2k47asxyv3w4ympmz2wy2cwjyzlal6936fjikf"))))
     (properties `((upstream-name . "ChemmineR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7520,6 +7555,8 @@ visualizing RNA-sequencing datasets and differentially expressed genes.")
        ("r-rcurl" ,r-rcurl)
        ("r-rjson" ,r-rjson)
        ("r-rsvg" ,r-rsvg)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://github.com/girke-lab/ChemmineR")
     (synopsis "Cheminformatics toolkit for R")
     (description
@@ -7535,14 +7572,14 @@ structures.")
 (define-public r-bioassayr
   (package
     (name "r-bioassayr")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bioassayR" version))
        (sha256
         (base32
-         "08vxkvxhqnryfbj4dwk3ifb9pn544www9zk2pj9fjbh5xfpwi7zw"))))
+         "1n0gsnxcl0lplqk8rs5ygxrxpx389ddl6wv3ciyz9g2xry5biyfy"))))
     (properties `((upstream-name . "bioassayR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7570,14 +7607,14 @@ available bioactivity data.")
 (define-public r-biobroom
   (package
     (name "r-biobroom")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biobroom" version))
        (sha256
         (base32
-         "1480ycdsh9xdhbpr47vdw5g6m8arqsnp8hc19wwhzm8npxh4qqlb"))))
+         "06qcrprn58kbrr5kyw1jl6z88b9w9g8xs6rkhrbnz8k7rv373fhf"))))
     (properties `((upstream-name . "biobroom")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7585,6 +7622,8 @@ available bioactivity data.")
        ("r-broom" ,r-broom)
        ("r-dplyr" ,r-dplyr)
        ("r-tidyr" ,r-tidyr)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://github.com/StoreyLab/biobroom")
     (synopsis "Turn Bioconductor objects into tidy data frames")
     (description
@@ -7600,14 +7639,14 @@ visualize bioinformatics analyses.")
 (define-public r-graphite
   (package
     (name "r-graphite")
-    (version "1.32.0")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "graphite" version))
        (sha256
         (base32
-         "1r9fk0cpdwm7012pa85dkjcpkml2j89zcznpf4hfdz66anfyyycd"))))
+         "0rc9cw3picz1y0lwhbzpk03ciij8kij74m15qgzh2ykla7zprb2p"))))
     (properties `((upstream-name . "graphite")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7627,14 +7666,14 @@ symbols).")
 (define-public r-reactomepa
   (package
     (name "r-reactomepa")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ReactomePA" version))
        (sha256
         (base32
-         "1vwc9kj1l4yi7c4f4lnq0i3wl2nrmmhcxyakz8qak122fi92z3j1"))))
+         "1ngilyn1mihwxs4sh5gk9y829xghdmh277cfw3vfgflz9sgwy21x"))))
     (properties `((upstream-name . "ReactomePA")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7646,6 +7685,8 @@ symbols).")
        ("r-graphite" ,r-graphite)
        ("r-igraph" ,r-igraph)
        ("r-reactome-db" ,r-reactome-db)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://guangchuangyu.github.io/software/ReactomePA")
     (synopsis "Reactome pathway analysis")
     (description
@@ -7657,14 +7698,14 @@ enrichment analysis and several functions for visualization.")
 (define-public r-ebarrays
   (package
     (name "r-ebarrays")
-    (version "2.50.0")
+    (version "2.52.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "EBarrays" version))
        (sha256
         (base32
-         "063rhsdp8x0f881kslq06zxfp6b2qabrz4vmfrn8a4v3pd3n7s13"))))
+         "00ld26bld8xgin9zqwxybahvhmqbrvr09jfphg0yr4j4zck6sqgf"))))
     (properties `((upstream-name . "EBarrays")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7681,14 +7722,14 @@ microarray data.")
 (define-public r-bioccasestudies
   (package
     (name "r-bioccasestudies")
-    (version "1.48.0")
+    (version "1.50.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocCaseStudies" version))
        (sha256
         (base32
-         "1sg9vxs24zfz3dg9y0qlrdsq43y0pbahbvcfxzlxjzjw80xzxpbd"))))
+         "0fadck1dk1zavpn9yrcwx6zgfi18fw5xfs8svgzipns6bq41j8ix"))))
     (properties
      `((upstream-name . "BiocCaseStudies")))
     (build-system r-build-system)
@@ -7703,14 +7744,14 @@ monograph.")
 (define-public r-biocgraph
   (package
     (name "r-biocgraph")
-    (version "1.48.0")
+    (version "1.50.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biocGraph" version))
        (sha256
         (base32
-         "1rv2lwiqwg7h7za23n896fs4dpla3xhw6kzwghb6iw5nlm2m61yw"))))
+         "1372bm4y3czqhpki10pnprxfkfncfcsy59zzvf8wj6q03acaavrj"))))
     (properties `((upstream-name . "biocGraph")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7728,14 +7769,14 @@ different graph related packages produced by Bioconductor.")
 (define-public r-experimenthub
   (package
     (name "r-experimenthub")
-    (version "1.12.0")
+    (version "1.14.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ExperimentHub" version))
        (sha256
         (base32
-         "054w2lkyirbmhgia0rp4nk9zzw3zphz6jxg6fc9zlarp90g64z24"))))
+         "1kgvprchz1fg8pl1irj62mk2gyb4jcc9iimpypv4c2iccy5bp84x"))))
     (properties `((upstream-name . "ExperimentHub")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7746,6 +7787,8 @@ different graph related packages produced by Bioconductor.")
        ("r-curl" ,r-curl)
        ("r-rappdirs" ,r-rappdirs)
        ("r-s4vectors" ,r-s4vectors)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://bioconductor.org/packages/ExperimentHub/")
     (synopsis "Client to access ExperimentHub resources")
     (description
@@ -7760,14 +7803,14 @@ access.")
 (define-public r-multiassayexperiment
   (package
     (name "r-multiassayexperiment")
-    (version "1.12.6")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MultiAssayExperiment" version))
        (sha256
         (base32
-         "174vzlxsyayb5il77cb3zzgszxl3l0wkprc9w6pgz4yv5ix13adi"))))
+         "0qlfnd86999jqv2nd0ikixi2sfd449dyg3ml4nbs8ycs57c2irgh"))))
     (properties
      `((upstream-name . "MultiAssayExperiment")))
     (build-system r-build-system)
@@ -7795,14 +7838,14 @@ rownames.")
 (define-public r-bioconcotk
   (package
     (name "r-bioconcotk")
-    (version "1.6.0")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocOncoTK" version))
        (sha256
         (base32
-         "0rnah6c01a33yb9663jim9iclan61rpcwprb56mykgn1pf5hywbj"))))
+         "021qzygfwdnd3naz1iqq01zr3zxv3k7wm1lklik24vc7axshxbmk"))))
     (properties `((upstream-name . "BiocOncoTK")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7828,6 +7871,8 @@ rownames.")
        ("r-scales" ,r-scales)
        ("r-shiny" ,r-shiny)
        ("r-summarizedexperiment" ,r-summarizedexperiment)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://bioconductor.org/packages/BiocOncoTK")
     (synopsis "Bioconductor components for general cancer genomics")
     (description
@@ -7838,20 +7883,22 @@ tools for genome-scale analysis of cancer studies.")
 (define-public r-biocor
   (package
     (name "r-biocor")
-    (version "1.10.0")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BioCor" version))
        (sha256
         (base32
-         "1bjw02rwmz2d715sgpfp08njb15200ch7cmipsf9hd5835ppg1jl"))))
+         "1xghclfqv8d23g72g8914br5zjx4sz9zihzczwwmpl15lghpnqwy"))))
     (properties `((upstream-name . "BioCor")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biocparallel" ,r-biocparallel)
        ("r-gseabase" ,r-gseabase)
        ("r-matrix" ,r-matrix)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://llrs.github.io/BioCor/")
     (synopsis "Functional similarities")
     (description
@@ -7865,14 +7912,14 @@ gene selection, testing relationships, and so on.")
 (define-public r-biocpkgtools
   (package
     (name "r-biocpkgtools")
-    (version "1.4.6")
+    (version "1.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocPkgTools" version))
        (sha256
         (base32
-         "0grwnmncmpqcplbfw3j210m1a8f7mmdizklh4zksg4ic21dpjj1a"))))
+         "0l5fvi1m4834n4h0iswbap135s9mpaiabw9czzn1r72ssz86vrcr"))))
     (properties `((upstream-name . "BiocPkgTools")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7915,14 +7962,14 @@ analytics on packages.")
 (define-public r-biocset
   (package
     (name "r-biocset")
-    (version "1.0.1")
+    (version "1.2.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocSet" version))
        (sha256
         (base32
-         "1xcksnvjflrdarn8xqmgf0n6wbsjkq9jazqwp35i52vqcq4ic1j9"))))
+         "041hq3rp0kv7kjwcjjrksk8lw3sj6j1v3wdcr8z611k0g0z6p0cj"))))
     (properties `((upstream-name . "BiocSet")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7933,6 +7980,8 @@ analytics on packages.")
        ("r-rlang" ,r-rlang)
        ("r-rtracklayer" ,r-rtracklayer)
        ("r-tibble" ,r-tibble)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page
      "https://bioconductor.org/packages/BiocSet")
     (synopsis
@@ -7948,14 +7997,14 @@ accessing web references for elements/sets are also available in BiocSet.")
 (define-public r-biocworkflowtools
   (package
     (name "r-biocworkflowtools")
-    (version "1.12.1")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocWorkflowTools" version))
        (sha256
         (base32
-         "0z28s572wg9qxv52dmixxz1xf1z3fyp2j7kzk0k32fp628918wr6"))))
+         "0p9r71ql67sdlgd5pv118lhz8b85pr5y4ijfwzcy8wrr8jwlbddy"))))
     (properties
      `((upstream-name . "BiocWorkflowTools")))
     (build-system r-build-system)
@@ -7981,14 +8030,14 @@ Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.")
 (define-public r-biodist
   (package
     (name "r-biodist")
-    (version "1.58.0")
+    (version "1.60.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bioDist" version))
        (sha256
         (base32
-         "0iabw07px3ybdgbbab0vv350051cm4aq8w47rz9dnmzx4kil9h5q"))))
+         "17bvxk0anvsp29j5nbblvaymf8qgbj3sz4ir2l7wj8kb8jfi19cp"))))
     (properties `((upstream-name . "bioDist")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8000,3 +8049,196 @@ Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.")
      "This package provides a collection of software tools for calculating
 distance measures.")
     (license license:artistic2.0)))
+
+(define-public r-pcatools
+  (package
+    (name "r-pcatools")
+    (version "2.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "PCAtools" version))
+       (sha256
+        (base32
+         "0mnwqrhm1hmhzwrpidf6z207w1ycpm572snvpp5swlg6hnxq6bnc"))))
+    (properties `((upstream-name . "PCAtools")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-beachmat" ,r-beachmat)
+       ("r-bh" ,r-bh)
+       ("r-biocparallel" ,r-biocparallel)
+       ("r-biocsingular" ,r-biocsingular)
+       ("r-cowplot" ,r-cowplot)
+       ("r-delayedarray" ,r-delayedarray)
+       ("r-delayedmatrixstats" ,r-delayedmatrixstats)
+       ("r-dqrng" ,r-dqrng)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-ggrepel" ,r-ggrepel)
+       ("r-lattice" ,r-lattice)
+       ("r-matrix" ,r-matrix)
+       ("r-rcpp" ,r-rcpp)
+       ("r-reshape2" ,r-reshape2)))
+    (native-inputs `(("r-knitr" ,r-knitr)))
+    (home-page "https://github.com/kevinblighe/PCAtools")
+    (synopsis "PCAtools: everything Principal Components Analysis")
+    (description
+     "@dfn{Principal Component Analysis} (PCA) extracts the fundamental
+structure of the data without the need to build any model to represent it.
+This \"summary\" of the data is arrived at through a process of reduction that
+can transform the large number of variables into a lesser number that are
+uncorrelated (i.e. the 'principal components'), while at the same time being
+capable of easy interpretation on the original data.  PCAtools provides
+functions for data exploration via PCA, and allows the user to generate
+publication-ready figures.  PCA is performed via @code{BiocSingular}; users
+can also identify an optimal number of principal components via different
+metrics, such as the elbow method and Horn's parallel analysis, which has
+relevance for data reduction in single-cell RNA-seq (scRNA-seq) and high
+dimensional mass cytometry data.")
+    (license license:gpl3)))
+
+(define-public r-rgreat
+  (package
+    (name "r-rgreat")
+    (version "1.20.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "rGREAT" version))
+       (sha256
+        (base32
+         "0n8dw9ibb2klsczcxvvinpi9l53w8cs436i0c8w2jmramayl593v"))))
+    (properties `((upstream-name . "rGREAT")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-genomicranges" ,r-genomicranges)
+       ("r-getoptlong" ,r-getoptlong)
+       ("r-iranges" ,r-iranges)
+       ("r-rcurl" ,r-rcurl)
+       ("r-rjson" ,r-rjson)))
+    (native-inputs `(("r-knitr" ,r-knitr)))
+    (home-page "https://github.com/jokergoo/rGREAT")
+    (synopsis "Client for GREAT analysis")
+    (description
+     "This package makes GREAT (Genomic Regions Enrichment of Annotations
+Tool) analysis automatic by constructing a HTTP POST request according to
+user's input and automatically retrieving results from GREAT web server.")
+    (license license:expat)))
+
+(define-public r-m3c
+  (package
+    (name "r-m3c")
+    (version "1.10.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "M3C" version))
+       (sha256
+        (base32
+         "0zq8lm4280p8h65i7myscwa4srs5ajh944xv6zni2f5sjyp7ij2y"))))
+    (properties `((upstream-name . "M3C")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-cluster" ,r-cluster)
+       ("r-corpcor" ,r-corpcor)
+       ("r-doparallel" ,r-doparallel)
+       ("r-dosnow" ,r-dosnow)
+       ("r-foreach" ,r-foreach)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-matrix" ,r-matrix)
+       ("r-matrixcalc" ,r-matrixcalc)
+       ("r-rtsne" ,r-rtsne)
+       ("r-umap" ,r-umap)))
+    (native-inputs `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/M3C")
+    (synopsis "Monte Carlo reference-based consensus clustering")
+    (description
+     "M3C is a consensus clustering algorithm that uses a Monte Carlo
+simulation to eliminate overestimation of @code{K} and can reject the null
+hypothesis @code{K=1}.")
+    (license license:agpl3+)))
+
+(define-public r-icens
+  (package
+    (name "r-icens")
+    (version "1.60.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "Icens" version))
+       (sha256
+        (base32
+         "0fh7wgkrw20f61p06i87nccnbig9wv4m0jcg7cx1rw7g2ndnabgp"))))
+    (properties `((upstream-name . "Icens")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-survival" ,r-survival)))
+    (home-page "https://bioconductor.org/packages/Icens")
+    (synopsis "NPMLE for censored and truncated data")
+    (description
+     "This package provides many functions for computing the
+@dfn{nonparametric maximum likelihood estimator} (NPMLE) for censored and
+truncated data.")
+    (license license:artistic2.0)))
+
+;; This is a CRAN package but it depends on r-icens, which is published on
+;; Bioconductor.
+(define-public r-interval
+  (package
+    (name "r-interval")
+    (version "1.1-0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "interval" version))
+       (sha256
+        (base32
+         "1lln9jkli28i4wivwzqrsxvv2n15560f7msjy5gssrm45vxrxms8"))))
+    (properties `((upstream-name . "interval")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-icens" ,r-icens)
+       ("r-mlecens" ,r-mlecens)
+       ("r-perm" ,r-perm)
+       ("r-survival" ,r-survival)))
+    (home-page "https://cran.r-project.org/web/packages/interval/")
+    (synopsis "Weighted Logrank tests and NPMLE for interval censored data")
+    (description
+     "This package provides functions to fit nonparametric survival curves,
+plot them, and perform logrank or Wilcoxon type tests.")
+    (license license:gpl2+)))
+
+;; This is a CRAN package, but it depends on r-interval, which depends on a
+;; Bioconductor package.
+(define-public r-fhtest
+  (package
+    (name "r-fhtest")
+    (version "1.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "FHtest" version))
+       (sha256
+        (base32
+         "1wsn0j9ydpp9nfswiqg21p09kgkvaq8fh0y0h8syqgizah7i8vs2"))))
+    (properties `((upstream-name . "FHtest")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-interval" ,r-interval)
+       ("r-kmsurv" ,r-kmsurv)
+       ("r-mass" ,r-mass)
+       ("r-perm" ,r-perm)
+       ("r-survival" ,r-survival)))
+    (home-page "https://cran.r-project.org/web/packages/FHtest/")
+    (synopsis "Tests for survival data based on the Fleming-Harrington class")
+    (description
+     "This package provides functions to compare two or more survival curves
+with:
+
+@itemize
+@item The Fleming-Harrington test for right-censored data based on
+  permutations and on counting processes.
+@item An extension of the Fleming-Harrington test for interval-censored data
+  based on a permutation distribution and on a score vector distribution.
+@end itemize
+")
+    (license license:gpl2+)))