X-Git-Url: https://git.hcoop.net/jackhill/guix/guix.git/blobdiff_plain/398c4a93471067698efc965d4de03d66b2b9738e..376d1fe759d95c02cc9158af4eb4d4890309be80:/gnu/packages/bioconductor.scm

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index d3ffd41a3c..fbaea6982b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -32,6 +32,8 @@
   #:use-module (gnu packages haskell)
   #:use-module (gnu packages image)
   #:use-module (gnu packages maths)
+  #:use-module (gnu packages netpbm)
+  #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages statistics)
   #:use-module (gnu packages web))
@@ -776,6 +778,30 @@ datasets which are derived from the Allen Brain Atlas:
 All datasets are restricted to protein coding genes.")
     (license license:gpl2+)))
 
+(define-public r-arrmdata
+  (package
+    (name "r-arrmdata")
+    (version "1.18.0")
+    (source (origin
+              (method url-fetch)
+              ;; We cannot use bioconductor-uri here because this tarball is
+              ;; located under "data/experiment/" instead of "bioc/".
+              (uri (string-append "https://www.bioconductor.org/packages/"
+                                  "release/data/experiment/src/contrib/"
+                                  "ARRmData_" version ".tar.gz"))
+              (sha256
+               (base32
+                "0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly"))))
+    (properties
+     `((upstream-name . "ARRmData")))
+    (build-system r-build-system)
+    (home-page "https://www.bioconductor.org/packages/ARRmData/")
+    (synopsis "Example dataset for normalization of Illumina 450k methylation data")
+    (description
+     "This package provides raw beta values from 36 samples across 3 groups
+from Illumina 450k methylation arrays.")
+    (license license:artistic2.0)))
+
 (define-public r-hsmmsinglecell
   (package
     (name "r-hsmmsinglecell")
@@ -815,13 +841,13 @@ resulting in a complete gene expression profile for each cell.")
 (define-public r-biocgenerics
   (package
     (name "r-biocgenerics")
-    (version "0.28.0")
+    (version "0.30.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocGenerics" version))
               (sha256
                (base32
-                "0cvpsrhg7sn7lpqgxvqrsagv6j7xj5rafq5xdjfd8zc4gxrs5rb8"))))
+                "1n87686bg5nmpqdpzwv1h551dkbxp9wk6wbmzpkgm71qxnk2yv9f"))))
     (properties
      `((upstream-name . "BiocGenerics")))
     (build-system r-build-system)
@@ -835,14 +861,14 @@ packages.")
 (define-public r-annotate
   (package
     (name "r-annotate")
-    (version "1.60.1")
+    (version "1.62.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "annotate" version))
        (sha256
         (base32
-         "0pk6ayr3vyqxk850ljkbyil4i382ngfqcbxlv0qrp62yfqgzcjwp"))))
+         "0hww0h4b7bv37mnjviazy247mnzj72z5linwm1gvljrgqv3bagcs"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
@@ -862,14 +888,14 @@ microarrays.")
 (define-public r-hpar
   (package
     (name "r-hpar")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "hpar" version))
        (sha256
         (base32
-         "1pm3k8apgynmdzv2d0chca3b636kcai3b1x861fyv1m3xs6msgxn"))))
+         "1mnld60nrn6qpb24sz2sy8vlw3wkhfc3z726gi67l8b5mdmkxgg5"))))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/hpar/")
     (synopsis "Human Protein Atlas in R")
@@ -880,14 +906,14 @@ the Human Protein Atlas project.")
 (define-public r-regioner
   (package
     (name "r-regioner")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "regioneR" version))
        (sha256
         (base32
-         "19la74swgzxp90z2nr3pzsgkxd7wp70zl6i2ipv3plg841f6k5zd"))))
+         "014h2q346ynfdbpavh4p69cyv4j65hk934liq5892zznjzl73z7p"))))
     (properties `((upstream-name . "regioneR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -909,14 +935,14 @@ region sets and other genomic features.")
 (define-public r-geneplotter
   (package
     (name "r-geneplotter")
-    (version "1.60.0")
+    (version "1.62.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "geneplotter" version))
        (sha256
         (base32
-         "10khr0pznxf3m0f5gzck9ymljrwcv3vamfmpskd51yjh36lhllqz"))))
+         "0jlqs20mqr0wgmjgzkzaynp3cy1z3xjzpz7055c1qi42fhimmimb"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotate" ,r-annotate)
@@ -934,14 +960,14 @@ region sets and other genomic features.")
 (define-public r-qvalue
   (package
     (name "r-qvalue")
-    (version "2.14.1")
+    (version "2.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "qvalue" version))
        (sha256
         (base32
-         "0kxavzm1j2mk26qicmjm90nxx4w5h3dxighzks7wzihay3k8cysc"))))
+         "00mahhwb4n2s6nycwkdkjs2qgyyyi7hyrby3qr269krprr6q3lh5"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-ggplot2" ,r-ggplot2)
@@ -963,14 +989,14 @@ problems in genomics, brain imaging, astrophysics, and data mining.")
 (define-public r-diffbind
   (package
     (name "r-diffbind")
-    (version "2.10.0")
+    (version "2.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DiffBind" version))
        (sha256
         (base32
-         "0j8pal40lr1gv8sss96hhkj7l1qn9sy4q4l2kqd4rfwl7qrcnfw5"))))
+         "1ialb1j2xa21a8dzss76qky83rg8y6jwdwi0mhy8b088zvxavich"))))
     (properties `((upstream-name . "DiffBind")))
     (build-system r-build-system)
     (inputs
@@ -992,11 +1018,11 @@ problems in genomics, brain imaging, astrophysics, and data mining.")
        ("r-locfit" ,r-locfit)
        ("r-rcolorbrewer" , r-rcolorbrewer)
        ("r-rcpp" ,r-rcpp)
+       ("r-rhtslib" ,r-rhtslib)
        ("r-rsamtools" ,r-rsamtools)
        ("r-s4vectors" ,r-s4vectors)
        ("r-summarizedexperiment" ,r-summarizedexperiment)
-       ("r-systempiper" ,r-systempiper)
-       ("r-zlibbioc" ,r-zlibbioc)))
+       ("r-systempiper" ,r-systempiper)))
     (home-page "http://bioconductor.org/packages/DiffBind")
     (synopsis "Differential binding analysis of ChIP-Seq peak data")
     (description
@@ -1008,14 +1034,14 @@ occupancy (overlap) analysis and plotting functions.")
 (define-public r-ripseeker
   (package
     (name "r-ripseeker")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RIPSeeker" version))
        (sha256
         (base32
-         "1x2n1iyik4s67bxq0fl6fpf602k51g4pxjpjpxkgx1a5fsk61f2i"))))
+         "0rfff4wal51iji0m74mgnrlcq6i41nq5b79mv5brv7mab3g0cv43"))))
     (properties `((upstream-name . "RIPSeeker")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1041,14 +1067,14 @@ processing to visualization and annotation.")
 (define-public r-multtest
   (package
     (name "r-multtest")
-    (version "2.38.0")
+    (version "2.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "multtest" version))
        (sha256
         (base32
-         "0lq62jw81hz9k840969n5byj57pwd0jqga3hqvhb6abb3g10yz7k"))))
+         "0vy9wk1111qm69xy4r4n01b9rw60dsrcj2169jd45yiq63cdq7bv"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-survival" ,r-survival)
@@ -1079,13 +1105,13 @@ expressed genes in DNA microarray experiments.")
 (define-public r-graph
   (package
     (name "r-graph")
-    (version "1.60.0")
+    (version "1.62.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "graph" version))
               (sha256
                (base32
-                "1kgnsm6f0vmb9qbkmmrnvxbwqc0gar17dq5gv1v10hrksw6mh64i"))))
+                "0rs81a8kp7nfzsfy2d11mlrjf4z156075p52wvz9nvi3vc6l348w"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)))
@@ -1181,12 +1207,12 @@ enrichedGO (addGeneIDs).")
 (define-public r-marray
   (package
     (name "r-marray")
-    (version "1.60.0")
+    (version "1.62.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "marray" version))
               (sha256
-               (base32 "1sh7l3c28x6zhdv99c9x05ii2yxmh9alkazp98kdi4fdb23rlzky"))))
+               (base32 "000745d7gxka8cx4jwxf0p128jk90dw6wi3y8dkrkyz2arkl29yz"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-limma" ,r-limma)))
@@ -1200,12 +1226,12 @@ normalization and quality checking.")
 (define-public r-cghbase
   (package
    (name "r-cghbase")
-   (version "1.42.0")
+   (version "1.44.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "CGHbase" version))
             (sha256
-             (base32 "0ghxp49xdi09p3f2qwrdrq2p4qjafj4z1rr08ycgbf11gb22h1sc"))))
+             (base32 "0z9lvn5dxym6kc8ak5fsqkipv2p4z49va3cyz1ch8rw477k2iwvm"))))
    (properties `((upstream-name . "CGHbase")))
    (build-system r-build-system)
    (propagated-inputs
@@ -1220,12 +1246,12 @@ the @code{arrayCGH} packages.")
 (define-public r-cghcall
   (package
    (name "r-cghcall")
-   (version "2.44.0")
+   (version "2.46.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "CGHcall" version))
             (sha256
-             (base32 "1k65kaiqvjyllzbpa2367n6f6kkmsy463kpflzs66hqhx2fshsmi"))))
+             (base32 "13vzk4myizs94hyak4iyxdrqyxyq1g85hwsmd13892g8pww6ga93"))))
    (properties `((upstream-name . "CGHcall")))
    (build-system r-build-system)
    (propagated-inputs
@@ -1243,12 +1269,12 @@ the @code{arrayCGH} packages.")
 (define-public r-qdnaseq
   (package
     (name "r-qdnaseq")
-    (version "1.18.0")
+    (version "1.20.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "QDNAseq" version))
               (sha256
-               (base32 "04ff9nbckzrlb45mr2j0c3mlh1wcggq5bbl81zklhq203c5x1wc2"))))
+               (base32 "02afy5bpj35981q1qm59jx399hksk6a9v1jfwy7x888rn86gfcfz"))))
     (properties `((upstream-name . "QDNAseq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1275,14 +1301,14 @@ respectively.")
 (define-public r-bayseq
   (package
     (name "r-bayseq")
-    (version "2.16.0")
+    (version "2.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "baySeq" version))
        (sha256
         (base32
-         "0f6yckihm5cwh3dycv2g54hf7nddhcqya4yrqwbir96y5k1d1km5"))))
+         "13lm7n5zqw8yg5sqb92h6ppcnr0l32qdgmv7i16pn32fb6z41p0w"))))
     (properties `((upstream-name . "baySeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1301,14 +1327,14 @@ more complex hypotheses) via empirical Bayesian methods.")
 (define-public r-chipcomp
   (package
     (name "r-chipcomp")
-    (version "1.12.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChIPComp" version))
        (sha256
         (base32
-         "1sypdsvwzssraanlhddhzpf9p0xs3qlflc0hp7yfbp0aplsifx85"))))
+         "0ragyl9dhg0ymgkh4z9d1cbwhbpcwh6x4985laaw6wmq2sjm732y"))))
     (properties `((upstream-name . "ChIPComp")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1335,14 +1361,14 @@ datasets.")
 (define-public r-riboprofiling
   (package
     (name "r-riboprofiling")
-    (version "1.12.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RiboProfiling" version))
        (sha256
         (base32
-         "1njvkd1khmf3rbp3dkz5z63wp79z4wmk4kzd3p3amky3w5by070z"))))
+         "1si8zkznm0slvghk786qsp0wd6sns6hggrnz88ww9fcfvsqvzsy9"))))
     (properties `((upstream-name . "RiboProfiling")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1374,14 +1400,14 @@ assessment, principal component analysis on codon coverage.")
 (define-public r-riboseqr
   (package
     (name "r-riboseqr")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "riboSeqR" version))
        (sha256
         (base32
-         "1nacsbsz77fw4a10nqj2ncsf25q3aaa0gd5w1q0ray2prx7qmlqb"))))
+         "1d1v098w7fmnsmxfg3l7yndyyr7ajig00axiwg413lyg255is1ga"))))
     (properties `((upstream-name . "riboSeqR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1402,14 +1428,14 @@ parsing of genetic sequencing data from ribosome profiling experiments.")
 (define-public r-interactionset
   (package
     (name "r-interactionset")
-    (version "1.10.0")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "InteractionSet" version))
        (sha256
         (base32
-         "0wirfhmpmkmnmhbqslw4bzvi2msqyqpjy1rrwr5qbd9k5rhx3bzb"))))
+         "0djgfpp34l6w8mk5b8s4wh0l12s4nn0f9ifvc3dq4970f6hb55z6"))))
     (properties
      `((upstream-name . "InteractionSet")))
     (build-system r-build-system)
@@ -1434,14 +1460,14 @@ experiments.")
 (define-public r-genomicinteractions
   (package
     (name "r-genomicinteractions")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GenomicInteractions" version))
        (sha256
         (base32
-         "0zy5isp2lqpjm0n0n1gly5bs4izn22yciibyqrnlrr60rmn5s67q"))))
+         "0ipvm3c1cqd46n60lsrqzf6fx4b3lwia57jyfx9wcqqg205qj73b"))))
     (properties
      `((upstream-name . "GenomicInteractions")))
     (build-system r-build-system)
@@ -1473,14 +1499,14 @@ information and producing various plots and statistics.")
 (define-public r-ctc
   (package
     (name "r-ctc")
-    (version "1.56.0")
+    (version "1.58.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ctc" version))
        (sha256
         (base32
-         "0yp7c0abk48jx1wf8n1gawh7dm15idahqc8va24v8cm0bzxgnmh2"))))
+         "15n5b6i18x14km5rdqiydxcak5cr5dr3adwwwc5kcqf5gkwmi3am"))))
     (build-system r-build-system)
     (propagated-inputs `(("r-amap" ,r-amap)))
     (home-page "https://bioconductor.org/packages/ctc/")
@@ -1493,14 +1519,14 @@ trees and clusters to other programs.")
 (define-public r-goseq
   (package
     (name "r-goseq")
-    (version "1.34.1")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "goseq" version))
        (sha256
         (base32
-         "1j87j98cajcjqabv6rb6zmcqxsqxxhbb3w60w1iink4rhsh8m3mn"))))
+         "0h8kd3d7yfdq8padfb0k92crwxi5h9gvgv4l3pa8k8wn4kczvciw"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
@@ -1519,14 +1545,14 @@ defined categories which are over/under represented in RNA-seq data.")
 (define-public r-glimma
   (package
     (name "r-glimma")
-    (version "1.10.1")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Glimma" version))
        (sha256
         (base32
-         "1ihrww55sa7ipi1rpp0rmn081sbqdwdmm5mz30zfrjr1xxqcdbcv"))))
+         "11qg5khqspxldfgg6p3xsxys472ab8wwi2snwc6bdxczv1f2p56x"))))
     (properties `((upstream-name . "Glimma")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1546,14 +1572,14 @@ information.")
 (define-public r-rots
   (package
     (name "r-rots")
-    (version "1.10.1")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ROTS" version))
        (sha256
         (base32
-         "1d5ggkk47xybcaizfy756qimbf2falg9cld46mhqjp3xfbfvzsg6"))))
+         "1j29pfyv2pn0wp544m5a568b3yd31kzavwwiwqylcjwvq5lfzy77"))))
     (properties `((upstream-name . "ROTS")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1570,14 +1596,14 @@ in omics data.")
 (define-public r-plgem
   (package
     (name "r-plgem")
-    (version "1.54.1")
+    (version "1.56.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "plgem" version))
        (sha256
         (base32
-         "1330635db3p8xm5y8fwrk1l37r6bgypsq70s3rx954i775zp6szg"))))
+         "0y6gp5rlkvlv435qps7zhih84g5wrdvg6myj74ywnpl5a773nfqp"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biobase" ,r-biobase)
@@ -1595,14 +1621,14 @@ genes or proteins in these datasets.")
 (define-public r-inspect
   (package
     (name "r-inspect")
-    (version "1.12.1")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "INSPEcT" version))
        (sha256
         (base32
-         "07q5msw9rnamx957mbiawnv3p9kr5ahwawzvv9xzla7d3lkk62xp"))))
+         "1a7smljndiyahgpj6vl079pvi3n0rfk1vkdkp799y4nm2wnhn93r"))))
     (properties `((upstream-name . "INSPEcT")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1637,14 +1663,14 @@ modeling the rates that determines changes in mature mRNA levels.")
 (define-public r-dnabarcodes
   (package
     (name "r-dnabarcodes")
-    (version "1.12.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DNABarcodes" version))
        (sha256
         (base32
-         "0g6j7ish0fk9jcib94wssjgp1m8ldcp42hyyg1ypr945fa3xghx0"))))
+         "1a0c9ag9n41cs0da9lfvpkxf7n5vbrfypaygdv66mw73aibix6v0"))))
     (properties `((upstream-name . "DNABarcodes")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1664,14 +1690,14 @@ demultiplexed, i.e. assigned to their original reference barcode.")
 (define-public r-ruvseq
   (package
     (name "r-ruvseq")
-    (version "1.16.1")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RUVSeq" version))
        (sha256
         (base32
-         "0qk7q3ab7k133divfkp54zsmvsmb9p8r09pkh2caswrzrn8achzv"))))
+         "0ln4qc9d5r15zlhazx6annx97c0wrx3jqpcvk7yj1jnwh349lw33"))))
     (properties `((upstream-name . "RUVSeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1690,20 +1716,22 @@ samples.")
 (define-public r-biocneighbors
   (package
     (name "r-biocneighbors")
-    (version "1.0.0")
+    (version "1.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocNeighbors" version))
        (sha256
         (base32
-         "1fsb96acidlxwf0h65xv7fnwdi58ckmq00gmwykrlawh88wgn1ll"))))
+         "08ak72y6mafzkhzfkx6b7waljpa0f1nxcrvyspd88sgzxgxjnkmg"))))
     (properties `((upstream-name . "BiocNeighbors")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocparallel" ,r-biocparallel)
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocparallel" ,r-biocparallel)
        ("r-rcpp" ,r-rcpp)
        ("r-rcppannoy" ,r-rcppannoy)
+       ("r-rcpphnsw" ,r-rcpphnsw)
        ("r-s4vectors" ,r-s4vectors)))
     (home-page "https://bioconductor.org/packages/BiocNeighbors")
     (synopsis "Nearest Neighbor Detection for Bioconductor packages")
@@ -1716,24 +1744,55 @@ to search for all neighbors within a given distance.  Parallelization is
 achieved for all methods using the BiocParallel framework.")
     (license license:gpl3)))
 
+(define-public r-biocsingular
+  (package
+    (name "r-biocsingular")
+    (version "1.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "BiocSingular" version))
+       (sha256
+        (base32
+         "129z6bkdhm5wlvrjiwrr8yl2jj9chh4i6dm6firlj4c4ql3jp4f5"))))
+    (properties `((upstream-name . "BiocSingular")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-beachmat" ,r-beachmat)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocparallel" ,r-biocparallel)
+       ("r-delayedarray" ,r-delayedarray)
+       ("r-irlba" ,r-irlba)
+       ("r-matrix" ,r-matrix)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rsvd" ,r-rsvd)
+       ("r-s4vectors" ,r-s4vectors)))
+    (home-page "https://github.com/LTLA/BiocSingular")
+    (synopsis "Singular value decomposition for Bioconductor packages")
+    (description
+     "This package implements exact and approximate methods for singular value
+decomposition and principal components analysis, in a framework that allows
+them to be easily switched within Bioconductor packages or workflows.  Where
+possible, parallelization is achieved using the BiocParallel framework.")
+    (license license:gpl3)))
+
 (define-public r-destiny
   (package
     (name "r-destiny")
-    (version "2.12.0")
+    (version "2.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "destiny" version))
        (sha256
         (base32
-         "1iay17mrhsfmpwl920rh1nip5b6ybva4h6bna0yld04paq5yva67"))))
+         "1bpa114fgrknn6415g4d1jrvb924nkwi18jzfqribpvcf1vlgrf3"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biobase" ,r-biobase)
        ("r-biocgenerics" ,r-biocgenerics)
-       ("r-fnn" ,r-fnn)
+       ("r-ggplot2" ,r-ggplot2)
        ("r-ggthemes" ,r-ggthemes)
-       ("r-hmisc" ,r-hmisc)
        ("r-igraph" ,r-igraph)
        ("r-matrix" ,r-matrix)
        ("r-proxy" ,r-proxy)
@@ -1754,14 +1813,14 @@ maps.")
 (define-public r-savr
   (package
     (name "r-savr")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "savR" version))
        (sha256
         (base32
-         "13bwq2a2pygdkmhrcmvz525wsi5i01j911711zgs6x93wj20b2w7"))))
+         "101p0c07p49c50lfnbfanyyikdypmqkvwclqifq32js9phqwhf6h"))))
     (properties `((upstream-name . "savR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1780,14 +1839,14 @@ Viewer (SAV) files, access data, and generate QC plots.")
 (define-public r-chipexoqual
   (package
     (name "r-chipexoqual")
-    (version "1.6.0")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChIPexoQual" version))
        (sha256
         (base32
-         "1773bpiybn4g9jlv46z29x19q4dpcvn7lairr3lq5pdqbqmz5hnp"))))
+         "02341i3lg74czgapf5qc6zvi2321af3rp85qavbg209fyc219acj"))))
     (properties `((upstream-name . "ChIPexoQual")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1818,13 +1877,13 @@ sequencing data.")
 (define-public r-copynumber
   (package
     (name "r-copynumber")
-    (version "1.22.0")
+    (version "1.24.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "copynumber" version))
               (sha256
                (base32
-                "0ipwj9i5p1bwhg5d80jdjagm02krpj2v0j47qdgw41h8wncdyal3"))))
+                "0gmxi7w776pjqv3v0pkdihb167zzrnr9hw64yfvzgjhkhrc6a4rp"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-s4vectors" ,r-s4vectors)
@@ -1841,14 +1900,14 @@ penalized least squares regression method.")
 (define-public r-dnacopy
   (package
     (name "r-dnacopy")
-    (version "1.56.0")
+    (version "1.58.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DNAcopy" version))
        (sha256
         (base32
-         "04cqdqxhva66xwh1s2vffi56b9fcrqd4slcrvqasj5lp2rkjli82"))))
+         "1gybr3cbsrqjgz00n4l5kb2nrmh302xpvzk5zk957ijj5qbfwmxa"))))
     (properties `((upstream-name . "DNAcopy")))
     (build-system r-build-system)
     (native-inputs `(("gfortran" ,gfortran)))
@@ -1892,14 +1951,14 @@ clusters).")
 (define-public r-deds
   (package
     (name "r-deds")
-    (version "1.56.0")
+    (version "1.58.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DEDS" version))
        (sha256
         (base32
-         "1zfgaar3bpss49zhs81mwlfzkx5lv92j8a64xd12ig88is24cw2c"))))
+         "029g7wgxc7yp1cdyalbi8gipkskrgp7nyl1s2whhjy5dqpfcpigs"))))
     (properties `((upstream-name . "DEDS")))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/DEDS/")
@@ -1941,14 +2000,14 @@ and regression inferences from RNA-sequencing data.")
 (define-public r-ebseq
   (package
     (name "r-ebseq")
-    (version "1.22.1")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "EBSeq" version))
        (sha256
         (base32
-         "1gzbk1hbwdan0j131ah88yryfvsiq0wqjnb09qbr4qaczpgvbad0"))))
+         "13rf85gffqn86r5gqibla3gqrnnag2zinrfawpcsgn3fk7hl3v83"))))
     (properties `((upstream-name . "EBSeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1965,14 +2024,14 @@ gene and isoform level using RNA-seq data")
 (define-public r-lpsymphony
   (package
     (name "r-lpsymphony")
-    (version "1.10.0")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "lpsymphony" version))
        (sha256
         (base32
-         "0vnsf5x6gvd1k8h89al7r6xbgbxsjbxphr675czzwggz79zbvq7y"))))
+         "13wvq4ip8nkyxmpncs6fzcf3vphra1n0fd5vz9kspbch0k1z6bsv"))))
     (build-system r-build-system)
     (inputs
      `(("gfortran" ,gfortran)
@@ -1995,14 +2054,14 @@ to install interface to SYMPHONY.")
 (define-public r-ihw
   (package
     (name "r-ihw")
-    (version "1.10.1")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "IHW" version))
        (sha256
         (base32
-         "10wqasl8k2j3y5qvak3xr2xj6symk656xww1y5n2l22nz832j19n"))))
+         "05hs6w1albkbyqzkid0bchb5zs41f31a7vhfbcswryhc86cxwzkz"))))
     (properties `((upstream-name . "IHW")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2025,14 +2084,14 @@ independent of the p-value under the null hypothesis.")
 (define-public r-icobra
   (package
     (name "r-icobra")
-    (version "1.10.0")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "iCOBRA" version))
        (sha256
         (base32
-         "0i1swrm31g0zffi5pm48bfvdfqpd32d0zdchkbyipz96al46jnld"))))
+         "1w9frnczgypzc2czbwrvlizqcqhbp6cdpyws7vkmnn9k0ggzxvfc"))))
     (properties `((upstream-name . "iCOBRA")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2059,18 +2118,19 @@ interactive exploration of results.")
 (define-public r-mast
   (package
     (name "r-mast")
-    (version "1.8.2")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MAST" version))
        (sha256
         (base32
-         "0rhx655dza0m6yg9jcfz2nmxqahvxx2l91kqgyp7qai0bzz9d9ix"))))
+         "0f2qkp346095k9m45frpd3bivrvaps9wlm0m3n0z8j0aj7w1kqlx"))))
     (properties `((upstream-name . "MAST")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-abind" ,r-abind)
+       ("r-blme" ,r-blme)
        ("r-biobase" ,r-biobase)
        ("r-biocgenerics" ,r-biocgenerics)
        ("r-data-table" ,r-data-table)
@@ -2092,14 +2152,14 @@ single cell assay data.")
 (define-public r-monocle
   (package
     (name "r-monocle")
-    (version "2.10.1")
+    (version "2.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "monocle" version))
        (sha256
         (base32
-         "0shwkgqs93j2l5h36yyvb1lf724107cfjrmzp5fxfj1lqc0y61lf"))))
+         "1rnr3k0wc61a806w9flapni91wz5xm0l66jabjzx0vbiwgczs32z"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biobase" ,r-biobase)
@@ -2147,14 +2207,14 @@ qPCR data, but could be used with other types as well.")
 (define-public r-noiseq
   (package
     (name "r-noiseq")
-    (version "2.26.1")
+    (version "2.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "NOISeq" version))
        (sha256
         (base32
-         "1wyhhi9ydlbjlz427093mdp5ppby77n37w5c2iyxlpsdk2m2nqsn"))))
+         "1k7k0xqa0lxj6mfsvbmd6x6glv9wynbwl87w5d3bilbq4dpc139j"))))
     (properties `((upstream-name . "NOISeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2174,14 +2234,14 @@ assumptions.")
 (define-public r-scdd
   (package
     (name "r-scdd")
-    (version "1.6.1")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scDD" version))
        (sha256
         (base32
-         "0dp2awajd5281dwpbs0wb8ij2pq9l60p0b80xhxrb41m5qybcri8"))))
+         "01hp6xxxap7541yi5dv596xvamqyyihvgkdy224ixa0n2cxyrhyf"))))
     (properties `((upstream-name . "scDD")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2210,14 +2270,14 @@ distributions.")
 (define-public r-scone
   (package
     (name "r-scone")
-    (version "1.6.1")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scone" version))
        (sha256
         (base32
-         "0l1x4cjnfjbpx6k55sjqx03555daa6v63rq0rg6b7jpz8xxzwa7p"))))
+         "00cr0jp1ywxygf2pryw7mmcmn7cp1500fvifkbwgg2qxbkq5zqck"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-aroma-light" ,r-aroma-light)
@@ -2250,14 +2310,14 @@ high-throughput analyses.")
 (define-public r-geoquery
   (package
     (name "r-geoquery")
-    (version "2.50.5")
+    (version "2.52.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GEOquery" version))
        (sha256
         (base32
-         "074dl00c8yi1ihpjkw7vl9vy2hggvipib0jn0hli0wrw7x1h9hg6"))))
+         "1r8x4jsl1mr9j7wyyqlj0zgwd80vkqhxxqrcgbb78ksryzq45jkr"))))
     (properties `((upstream-name . "GEOquery")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2281,14 +2341,14 @@ the bridge between GEO and BioConductor.")
 (define-public r-illuminaio
   (package
     (name "r-illuminaio")
-    (version "0.24.0")
+    (version "0.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "illuminaio" version))
        (sha256
         (base32
-         "1rdp9b4xlv91yzba7pd7k50s3nkljfxmdmyz5jl0j8ybhmpl6rns"))))
+         "18plm8p40gfzfmqflxssrdj8az3xvmnmh9i9dafl3af3bxwv03l8"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-base64" ,r-base64)))
@@ -2302,18 +2362,19 @@ files, including IDAT.")
 (define-public r-siggenes
   (package
     (name "r-siggenes")
-    (version "1.56.0")
+    (version "1.58.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "siggenes" version))
        (sha256
         (base32
-         "0cjlb5r04x15xkhk00i3wvpx21kj0k29pn0mj3whwqk31zznnk1b"))))
+         "178jmmdxsv3rd71a9w5yrvg5aplak40hb42vna15g1d55c2yv1ib"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biobase" ,r-biobase)
-       ("r-multtest" ,r-multtest)))
+       ("r-multtest" ,r-multtest)
+       ("r-scrime" ,r-scrime)))
     (home-page "https://bioconductor.org/packages/siggenes/")
     (synopsis
      "Multiple testing using SAM and Efron's empirical Bayes approaches")
@@ -2327,14 +2388,14 @@ Bayes Analyses of Microarrays} (EBAM).")
 (define-public r-bumphunter
   (package
     (name "r-bumphunter")
-    (version "1.24.5")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bumphunter" version))
        (sha256
         (base32
-         "1f9vk3srffbx8jpza40nd18a4y0p0z8q40mx55dlcnddkwrqi19b"))))
+         "1dkyicwqdaahnxcxj6kmivkqb47yccx51lb1q0yar3xpw91vwlfx"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
@@ -2361,14 +2422,14 @@ studies.")
 (define-public r-minfi
   (package
     (name "r-minfi")
-    (version "1.28.4")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "minfi" version))
        (sha256
         (base32
-         "1sjwwqb0syngvj75saaky9y06hbxsawhhcmfvavzkhicxipafv7r"))))
+         "0qir0zd0qa97fzm33v10nyrsjp8nmzhn7mn20dnlpsg7rwlf60pd"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-beanplot" ,r-beanplot)
@@ -2410,14 +2471,14 @@ methylation arrays.")
 (define-public r-methylumi
   (package
     (name "r-methylumi")
-    (version "2.28.0")
+    (version "2.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "methylumi" version))
        (sha256
         (base32
-         "14p2qi18cprfvb2gxng1vm48c7zwh23h88q9qjgipj9xl5axsgw2"))))
+         "13acn771ybi10v50x123bq5yqd62b8sr4gz77lpgaj192sxq9d9f"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotate" ,r-annotate)
@@ -2454,14 +2515,14 @@ and Infinium HD arrays are also included.")
 (define-public r-lumi
   (package
     (name "r-lumi")
-    (version "2.34.0")
+    (version "2.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "lumi" version))
        (sha256
         (base32
-         "1fpmjpgcy5n0hx9whn9m3jhjmciqq0l59nvy5addbq0a4wnjhx8q"))))
+         "1rf6xmd2wnajjvnl50q63agakzjf4hrzn2chdsnhapi7fh7bcjba"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-affy" ,r-affy)
@@ -2493,14 +2554,14 @@ especially Illumina Infinium methylation microarrays.")
 (define-public r-linnorm
   (package
     (name "r-linnorm")
-    (version "2.6.1")
+    (version "2.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Linnorm" version))
        (sha256
         (base32
-         "1qgk8m5kc409flqxs3vnf228v3z0112q8py9hgfgyiwvi6yzdbp6"))))
+         "1rv3ljdwb71364qd2p8za3jpk08agvzwas6f63s5d8wjlapzm3i5"))))
     (properties `((upstream-name . "Linnorm")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2552,14 +2613,14 @@ evaluation of DEG analysis methods.")
 (define-public r-ioniser
   (package
     (name "r-ioniser")
-    (version "2.6.0")
+    (version "2.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "IONiseR" version))
        (sha256
         (base32
-         "01lqisdlsvym8nhgpzn7lpcddk9lv9253dy9v65r2dicb5xqhj00"))))
+         "0kznyqqpm0zbah537p197z1cgrgh9w82whmq0aydfxzgs2vxdw2y"))))
     (properties `((upstream-name . "IONiseR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2624,14 +2685,14 @@ kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
 (define-public r-triform
   (package
     (name "r-triform")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "triform" version))
        (sha256
         (base32
-         "12ca24pv1r5vbw3rq345jqg7x3prrbsxk6445zikpzfblwmw0b4s"))))
+         "0bsxkn386kfx4gg19p6smy5fi3k7xdw89r5hvfsks8hsdpdz3hya"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)
@@ -2648,14 +2709,14 @@ peak definition in combination with known profile characteristics.")
 (define-public r-varianttools
   (package
     (name "r-varianttools")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "VariantTools" version))
        (sha256
         (base32
-         "1ml3pl7xnxvzr6zkypr80xzw6nffswk29gzxycn42473sc4ixn7j"))))
+         "0y37nziipwikg47x4jhhsx0dyv15rrih4a4z43jbzv4jgq4krzql"))))
     (properties `((upstream-name . "VariantTools")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2688,14 +2749,14 @@ gmapR.")
 (define-public r-heatplus
   (package
     (name "r-heatplus")
-    (version "2.28.0")
+    (version "2.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Heatplus" version))
        (sha256
         (base32
-         "0drspjzgb23ra2kdvpxhsd8mdifsf97fcf668llyz2hr0r39fc48"))))
+         "18b0zy12przp88sj1smvfdd39m17nhhnqzk656bs5pjls2ifmcm6"))))
     (properties `((upstream-name . "Heatplus")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2925,14 +2986,14 @@ profiles (GO and KEGG) of gene and gene clusters.")
 (define-public r-mlinterfaces
   (package
     (name "r-mlinterfaces")
-    (version "1.62.0")
+    (version "1.62.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MLInterfaces" version))
        (sha256
         (base32
-         "12bgplyzfh0hkwmdp5w4cs5zw3ygdhzmiqzm8vhjyni6m9nrxwy8"))))
+         "1h0x1p2h8x1h276wxx6kcnb4c4s5sglnmd58iigl81a224x8gxwp"))))
     (properties `((upstream-name . "MLInterfaces")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3654,7 +3715,7 @@ visualization with image data.")
     (synopsis "Tools for high-throughput metabolomics")
     (description
      "This package provides tools to analyze and visualize high-throughput
-metabolomics data aquired using chromatography-mass spectrometry.  These tools
+metabolomics data acquired using chromatography-mass spectrometry.  These tools
 preprocess data in a way that enables reliable and powerful differential
 analysis.")
     (license license:artistic2.0)))
@@ -3685,3 +3746,593 @@ dimensional data which are represented as tracks describe different features
 from different aspects.  This package provides high flexibility to arrange
 genomic categories and to add self-defined graphics in the plot.")
     (license license:expat)))
+
+(define-public r-somaticsignatures
+  (package
+    (name "r-somaticsignatures")
+    (version "2.18.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "SomaticSignatures" version))
+       (sha256
+        (base32
+         "013dslbyq55a41d3n842brjk2bq1kxw0r18mb6drgbxx2sflzc02"))))
+    (properties
+     `((upstream-name . "SomaticSignatures")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-biostrings" ,r-biostrings)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-ggbio" ,r-ggbio)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-iranges" ,r-iranges)
+       ("r-nmf" ,r-nmf)
+       ("r-pcamethods" ,r-pcamethods)
+       ("r-proxy" ,r-proxy)
+       ("r-reshape2" ,r-reshape2)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-variantannotation" ,r-variantannotation)))
+    (home-page "https://github.com/juliangehring/SomaticSignatures")
+    (synopsis "Somatic signatures")
+    (description
+     "This package identifies mutational signatures of @dfn{single nucleotide
+variants} (SNVs).  It provides a infrastructure related to the methodology
+described in Nik-Zainal (2012, Cell), with flexibility in the matrix
+decomposition algorithms.")
+    (license license:expat)))
+
+(define-public r-yapsa
+  (package
+    (name "r-yapsa")
+    (version "1.8.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "YAPSA" version))
+       (sha256
+        (base32
+         "1agacimdd1m5yja2xbcsb83mns4svpxbjcsfrvm9ydqdj737i10j"))))
+    (properties `((upstream-name . "YAPSA")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-circlize" ,r-circlize)
+       ("r-complexheatmap" ,r-complexheatmap)
+       ("r-corrplot" ,r-corrplot)
+       ("r-dendextend" ,r-dendextend)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-getoptlong" ,r-getoptlong)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-gridextra" ,r-gridextra)
+       ("r-gtrellis" ,r-gtrellis)
+       ("r-keggrest" ,r-keggrest)
+       ("r-lsei" ,r-lsei)
+       ("r-pmcmr" ,r-pmcmr)
+       ("r-reshape2" ,r-reshape2)
+       ("r-somaticsignatures" ,r-somaticsignatures)
+       ("r-variantannotation" ,r-variantannotation)))
+    (home-page "https://bioconductor.org/packages/YAPSA/")
+    (synopsis "Yet another package for signature analysis")
+    (description
+     "This package provides functions and routines useful in the analysis of
+somatic signatures (cf. L. Alexandrov et al., Nature 2013).  In particular,
+functions to perform a signature analysis with known signatures and a
+signature analysis on @dfn{stratified mutational catalogue} (SMC) are
+provided.")
+    (license license:gpl3)))
+
+(define-public r-gcrma
+  (package
+    (name "r-gcrma")
+    (version "2.54.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "gcrma" version))
+       (sha256
+        (base32
+         "1v5fi98gdmj002ryq0rgsg2l4x3m3w5pz4h3bx4v8lk15azafgim"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-affy" ,r-affy)
+       ("r-affyio" ,r-affyio)
+       ("r-biobase" ,r-biobase)
+       ("r-biocmanager" ,r-biocmanager)
+       ("r-biostrings" ,r-biostrings)
+       ("r-xvector" ,r-xvector)))
+    (home-page "https://bioconductor.org/packages/gcrma/")
+    (synopsis "Background adjustment using sequence information")
+    (description
+     "Gcrma adjusts for background intensities in Affymetrix array data which
+include optical noise and @dfn{non-specific binding} (NSB).  The main function
+@code{gcrma} converts background adjusted probe intensities to expression
+measures using the same normalization and summarization methods as a
+@dfn{Robust Multiarray Average} (RMA).  Gcrma uses probe sequence information
+to estimate probe affinity to NSB.  The sequence information is summarized in
+a more complex way than the simple GC content.  Instead, the base types (A, T,
+G or C) at each position along the probe determine the affinity of each probe.
+The parameters of the position-specific base contributions to the probe
+affinity is estimated in an NSB experiment in which only NSB but no
+gene-specific bidning is expected.")
+    ;; Any version of the LGPL
+    (license license:lgpl2.1+)))
+
+(define-public r-simpleaffy
+  (package
+    (name "r-simpleaffy")
+    (version "2.58.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "simpleaffy" version))
+       (sha256
+        (base32
+         "0bry0d2vw0w2rrpnmfm1kl5v4rdclypmy33jvs9l43vd6vx2ra9s"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-affy" ,r-affy)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-gcrma" ,r-gcrma)
+       ("r-genefilter" ,r-genefilter)))
+    (home-page "https://bioconductor.org/packages/simpleaffy/")
+    (synopsis "Very simple high level analysis of Affymetrix data")
+    (description
+     "This package provides high level functions for reading Affy @file{.CEL}
+files, phenotypic data, and then computing simple things with it, such as
+t-tests, fold changes and the like.  It makes heavy use of the @code{affy}
+library.  It also has some basic scatter plot functions and mechanisms for
+generating high resolution journal figures.")
+    (license license:gpl2+)))
+
+(define-public r-yaqcaffy
+  (package
+    (name "r-yaqcaffy")
+    (version "1.42.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "yaqcaffy" version))
+       (sha256
+        (base32
+         "192n1zvd54nm9q71vyb6dcr7ia6givf4bjwf6542jjig085lwhxk"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-simpleaffy" ,r-simpleaffy)))
+    (home-page "https://bioconductor.org/packages/yaqcaffy/")
+    (synopsis "Affymetrix quality control and reproducibility analysis")
+    (description
+     "This is a package that can be used for quality control of Affymetrix
+GeneChip expression data and reproducibility analysis of human whole genome
+chips with the MAQC reference datasets.")
+    (license license:artistic2.0)))
+
+(define-public r-quantro
+  (package
+    (name "r-quantro")
+    (version "1.16.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "quantro" version))
+       (sha256
+        (base32
+         "1777gjgn855f04yv7hx70h9l8idmjzamkpazaq2cdr8qzhxwy2ib"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-doparallel" ,r-doparallel)
+       ("r-foreach" ,r-foreach)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-iterators" ,r-iterators)
+       ("r-minfi" ,r-minfi)
+       ("r-rcolorbrewer" ,r-rcolorbrewer)))
+    (home-page "https://bioconductor.org/packages/quantro/")
+    (synopsis "Test for when to use quantile normalization")
+    (description
+     "This package provides a data-driven test for the assumptions of quantile
+normalization using raw data such as objects that inherit eSets (e.g.
+ExpressionSet, MethylSet).  Group level information about each sample (such as
+Tumor / Normal status) must also be provided because the test assesses if
+there are global differences in the distributions between the user-defined
+groups.")
+    (license license:gpl3+)))
+
+(define-public r-yarn
+  (package
+    (name "r-yarn")
+    (version "1.8.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "yarn" version))
+       (sha256
+        (base32
+         "0c84x1zq34hadpsyaa873r8kg0jcxp09c2z63377hlmhsll90l7s"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-biomart" ,r-biomart)
+       ("r-downloader" ,r-downloader)
+       ("r-edger" ,r-edger)
+       ("r-gplots" ,r-gplots)
+       ("r-limma" ,r-limma)
+       ("r-matrixstats" ,r-matrixstats)
+       ("r-preprocesscore" ,r-preprocesscore)
+       ("r-quantro" ,r-quantro)
+       ("r-rcolorbrewer" ,r-rcolorbrewer)
+       ("r-readr" ,r-readr)))
+    (home-page "https://bioconductor.org/packages/yarn/")
+    (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization")
+    (description
+     "Expedite large RNA-Seq analyses using a combination of previously
+developed tools.  YARN is meant to make it easier for the user in performing
+basic mis-annotation quality control, filtering, and condition-aware
+normalization.  YARN leverages many Bioconductor tools and statistical
+techniques to account for the large heterogeneity and sparsity found in very
+large RNA-seq experiments.")
+    (license license:artistic2.0)))
+
+(define-public r-roar
+  (package
+    (name "r-roar")
+    (version "1.18.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "roar" version))
+       (sha256
+        (base32
+         "15650s9vs7dvmqpvrs4xwn6j4kh14yqsx4daqyhhxxr68kn8mklw"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicalignments" ,r-genomicalignments)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+    (home-page "https://github.com/vodkatad/roar/")
+    (synopsis "Identify differential APA usage from RNA-seq alignments")
+    (description
+     "This package provides tools for identifying preferential usage of APA
+sites, comparing two biological conditions, starting from known alternative
+sites and alignments obtained from standard RNA-seq experiments.")
+    (license license:gpl3)))
+
+(define-public r-xbseq
+  (package
+    (name "r-xbseq")
+    (version "1.14.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "XBSeq" version))
+       (sha256
+        (base32
+         "0na0jiqfy40bzl243gqc2214k4hibv6v4ndiqwq0c5f78cyr6lph"))))
+    (properties `((upstream-name . "XBSeq")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-deseq2" ,r-deseq2)
+       ("r-dplyr" ,r-dplyr)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-locfit" ,r-locfit)
+       ("r-magrittr" ,r-magrittr)
+       ("r-matrixstats" ,r-matrixstats)
+       ("r-pracma" ,r-pracma)
+       ("r-roar" ,r-roar)))
+    (home-page "https://github.com/Liuy12/XBSeq")
+    (synopsis "Test for differential expression for RNA-seq data")
+    (description
+     "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential
+expression} (DE), where a statistical model was established based on the
+assumption that observed signals are the convolution of true expression
+signals and sequencing noises.  The mapped reads in non-exonic regions are
+considered as sequencing noises, which follows a Poisson distribution.  Given
+measurable observed signal and background noise from RNA-seq data, true
+expression signals, assuming governed by the negative binomial distribution,
+can be delineated and thus the accurate detection of differential expressed
+genes.")
+    (license license:gpl3+)))
+
+(define-public r-massspecwavelet
+  (package
+    (name "r-massspecwavelet")
+    (version "1.48.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "MassSpecWavelet" version))
+       (sha256
+        (base32
+         "1xcr568a36b570rldy27wq4a2jn7yf5f6fddlzgx6x944jdn3ckz"))))
+    (properties
+     `((upstream-name . "MassSpecWavelet")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-waveslim" ,r-waveslim)))
+    (home-page "https://bioconductor.org/packages/MassSpecWavelet/")
+    (synopsis "Mass spectrum processing by wavelet-based algorithms")
+    (description
+     "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS)
+data mainly through the use of wavelet transforms.  It supports peak detection
+based on @dfn{Continuous Wavelet Transform} (CWT).")
+    (license license:lgpl2.0+)))
+
+(define-public r-xcms
+  (package
+    (name "r-xcms")
+    (version "3.4.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "xcms" version))
+       (sha256
+        (base32
+         "073f25m7y8z4560k93d99fv72pr7nrgrp054zssi7jhas4l3ddww"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocparallel" ,r-biocparallel)
+       ("r-lattice" ,r-lattice)
+       ("r-massspecwavelet" ,r-massspecwavelet)
+       ("r-msnbase" ,r-msnbase)
+       ("r-multtest" ,r-multtest)
+       ("r-mzr" ,r-mzr)
+       ("r-plyr" ,r-plyr)
+       ("r-protgenerics" ,r-protgenerics)
+       ("r-rann" ,r-rann)
+       ("r-rcolorbrewer" ,r-rcolorbrewer)
+       ("r-robustbase" ,r-robustbase)
+       ("r-s4vectors" ,r-s4vectors)))
+    (home-page "https://bioconductor.org/packages/xcms/")
+    (synopsis "LC/MS and GC/MS mass spectrometry data analysis")
+    (description
+     "This package provides a framework for processing and visualization of
+chromatographically separated and single-spectra mass spectral data.  It
+imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files.  It preprocesses
+data for high-throughput, untargeted analyte profiling.")
+    (license license:gpl2+)))
+
+(define-public r-wrench
+  (package
+    (name "r-wrench")
+    (version "1.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "Wrench" version))
+       (sha256
+        (base32
+         "12gfdj2p52pah67bimz14xcwmcb4c2snjwswj0fns7v3v1h9rlqg"))))
+    (properties `((upstream-name . "Wrench")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-limma" ,r-limma)
+       ("r-locfit" ,r-locfit)
+       ("r-matrixstats" ,r-matrixstats)))
+    (home-page "https://github.com/HCBravoLab/Wrench")
+    (synopsis "Wrench normalization for sparse count data")
+    (description
+     "Wrench is a package for normalization sparse genomic count data, like
+that arising from 16s metagenomic surveys.")
+    (license license:artistic2.0)))
+
+(define-public r-wiggleplotr
+  (package
+    (name "r-wiggleplotr")
+    (version "1.6.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "wiggleplotr" version))
+       (sha256
+        (base32
+         "12fhbskkjwv4d9bdy3gab8n9pcf7qpwiwgx0248as445vfw8dil3"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-assertthat" ,r-assertthat)
+       ("r-cowplot" ,r-cowplot)
+       ("r-dplyr" ,r-dplyr)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-iranges" ,r-iranges)
+       ("r-purrr" ,r-purrr)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-s4vectors" ,r-s4vectors)))
+    (home-page "https://bioconductor.org/packages/wiggleplotr/")
+    (synopsis "Make read coverage plots from BigWig files")
+    (description
+     "This package provides tools to visualize read coverage from sequencing
+experiments together with genomic annotations (genes, transcripts, peaks).
+Introns of long transcripts can be rescaled to a fixed length for better
+visualization of exonic read coverage.")
+    (license license:asl2.0)))
+
+(define-public r-widgettools
+  (package
+    (name "r-widgettools")
+    (version "1.60.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "widgetTools" version))
+       (sha256
+        (base32
+         "0mz69pdr6q69avsvs6r5ncdkdmgwfislpil4v18dsflw4j454gwf"))))
+    (properties `((upstream-name . "widgetTools")))
+    (build-system r-build-system)
+    (home-page "https://bioconductor.org/packages/widgetTools/")
+    (synopsis "Tools for creating interactive tcltk widgets")
+    (description
+     "This packages contains tools to support the construction of tcltk
+widgets in R.")
+    ;; Any version of the LGPL.
+    (license license:lgpl3+)))
+
+(define-public r-webbioc
+  (package
+    (name "r-webbioc")
+    (version "1.54.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "webbioc" version))
+       (sha256
+        (base32
+         "16n6wc9q51wfpmh9y77p53sqdqdd8pn50c67vf6h4n7gv5wgnpwi"))))
+    (build-system r-build-system)
+    (inputs
+     `(("netpbm" ,netpbm)
+       ("perl" ,perl)))
+    (propagated-inputs
+     `(("r-affy" ,r-affy)
+       ("r-annaffy" ,r-annaffy)
+       ("r-biobase" ,r-biobase)
+       ("r-biocmanager" ,r-biocmanager)
+       ("r-gcrma" ,r-gcrma)
+       ("r-multtest" ,r-multtest)
+       ("r-qvalue" ,r-qvalue)
+       ("r-vsn" ,r-vsn)))
+    (home-page "https://www.bioconductor.org/")
+    (synopsis "Bioconductor web interface")
+    (description
+     "This package provides an integrated web interface for doing microarray
+analysis using several of the Bioconductor packages.  It is intended to be
+deployed as a centralized bioinformatics resource for use by many users.
+Currently only Affymetrix oligonucleotide analysis is supported.")
+    (license license:gpl2+)))
+
+(define-public r-zfpkm
+  (package
+    (name "r-zfpkm")
+    (version "1.4.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "zFPKM" version))
+       (sha256
+        (base32
+         "0rvfrjxxvfng9fxxn316gm96v4rahx62vlk3axr2bzjbi1r4s8v5"))))
+    (properties `((upstream-name . "zFPKM")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-checkmate" ,r-checkmate)
+       ("r-dplyr" ,r-dplyr)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)
+       ("r-tidyr" ,r-tidyr)))
+    (home-page "https://github.com/ronammar/zFPKM/")
+    (synopsis "Functions to facilitate zFPKM transformations")
+    (description
+     "This is a package to perform the zFPKM transform on RNA-seq FPKM data.
+This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
+24215113).")
+    (license license:gpl3)))
+
+(define-public r-rbowtie2
+  (package
+    (name "r-rbowtie2")
+    (version "1.4.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "Rbowtie2" version))
+       (sha256
+        (base32
+         "045cmfwqzcj4zn6r16hkpmr5sd5y0mxvrs5yynf460fdz2p418cr"))))
+    (properties `((upstream-name . "Rbowtie2")))
+    (build-system r-build-system)
+    (inputs
+     `(("zlib" ,zlib)))
+    (home-page "https://bioconductor.org/packages/Rbowtie2/")
+    (synopsis "R wrapper for Bowtie2 and AdapterRemoval")
+    (description
+     "This package provides an R wrapper of the popular @code{bowtie2}
+sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for
+rapid adapter trimming, identification, and read merging.")
+    (license license:gpl3+)))
+
+(define-public r-progeny
+  (package
+    (name "r-progeny")
+    (version "1.4.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "progeny" version))
+       (sha256
+        (base32
+         "02z09rbzi305jrwzai8zayxi82563lxcaldp4r9pw564qkbl7pk7"))))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-biobase" ,r-biobase)))
+    (home-page "https://github.com/saezlab/progeny")
+    (synopsis "Pathway responsive gene activity inference")
+    (description
+     "This package provides a function to infer pathway activity from gene
+expression.  It contains the linear model inferred in the publication
+\"Perturbation-response genes reveal signaling footprints in cancer gene
+expression\".")
+    (license license:asl2.0)))
+
+(define-public r-arrmnormalization
+  (package
+    (name "r-arrmnormalization")
+    (version "1.22.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "ARRmNormalization" version))
+       (sha256
+        (base32
+         "09wfd4vqfvmkpqn9dwqly1dz4h1ckh621jbwj1dab6q4z0dfmzmd"))))
+    (properties
+     `((upstream-name . "ARRmNormalization")))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-arrmdata" ,r-arrmdata)))
+    (home-page "https://bioconductor.org/packages/ARRmNormalization/")
+    (synopsis "Adaptive robust regression normalization for methylation data")
+    (description
+     "This is a package to perform the @dfn{Adaptive Robust Regression
+method} (ARRm) for the normalization of methylation data from the Illumina
+Infinium HumanMethylation 450k assay.")
+    (license license:artistic2.0)))
+
+(define-public r-biocfilecache
+  (package
+    (name "r-biocfilecache")
+    (version "1.8.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "BiocFileCache" version))
+       (sha256
+        (base32
+         "1mi8p8hvrdxim8lqsid2cb7284imyjf9rlzsrdlzdjac7dp9bpdb"))))
+    (properties `((upstream-name . "BiocFileCache")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-curl" ,r-curl)
+       ("r-dbi" ,r-dbi)
+       ("r-dbplyr" ,r-dbplyr)
+       ("r-dplyr" ,r-dplyr)
+       ("r-httr" ,r-httr)
+       ("r-rappdirs" ,r-rappdirs)
+       ("r-rsqlite" ,r-rsqlite)))
+    (home-page "https://bioconductor.org/packages/BiocFileCache/")
+    (synopsis "Manage files across sessions")
+    (description
+     "This package creates a persistent on-disk cache of files that the user
+can add, update, and retrieve.  It is useful for managing resources (such as
+custom Txdb objects) that are costly or difficult to create, web resources,
+and data files used across sessions.")
+    (license license:artistic2.0)))