gnu: r-rhisat2: Update to 1.0.1.

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

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 3561f8c..b488839 100644 (file)
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -24,6 +24,7 @@
   #:use-module (guix download)
   #:use-module (guix build-system r)
   #:use-module (gnu packages)
+  #:use-module (gnu packages base)
   #:use-module (gnu packages bioinformatics)
   #:use-module (gnu packages cran)
   #:use-module (gnu packages compression)
@@ -906,14 +907,14 @@ the Human Protein Atlas project.")
 (define-public r-regioner
   (package
     (name "r-regioner")
-    (version "1.16.0")
+    (version "1.16.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "regioneR" version))
        (sha256
         (base32
-         "014h2q346ynfdbpavh4p69cyv4j65hk934liq5892zznjzl73z7p"))))
+         "1b8ybx4wcxlqw9nvajawsf0lqaqn9v89rxcawg4g3dbzlfssfc5q"))))
     (properties `((upstream-name . "regioneR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1152,44 +1153,45 @@ determining dependencies between variables, code improvement suggestions.")
 (define-public r-chippeakanno
   (package
     (name "r-chippeakanno")
-    (version "3.16.1")
+    (version "3.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChIPpeakAnno" version))
        (sha256
         (base32
-         "1x98d8iwrxjwdz1s5cnvi6flynw9gdkmara9gwf205qxgmy7j3a3"))))
+         "089v16mm5m0rlyyyd0d6rz8gwb852zf3bcdrrw70wanlfjn258q7"))))
     (properties `((upstream-name . "ChIPpeakAnno")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
        ("r-biocmanager" ,r-biocmanager)
-       ("r-biostrings" ,r-biostrings)
-       ("r-delayedarray" ,r-delayedarray)
-       ("r-go-db" ,r-go-db)
        ("r-biomart" ,r-biomart)
+       ("r-biostrings" ,r-biostrings)
        ("r-bsgenome" ,r-bsgenome)
+       ("r-dbi" ,r-dbi)
+       ("r-delayedarray" ,r-delayedarray)
+       ("r-ensembldb" ,r-ensembldb)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicalignments" ,r-genomicalignments)
        ("r-genomicfeatures" ,r-genomicfeatures)
        ("r-genomicranges" ,r-genomicranges)
-       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-go-db" ,r-go-db)
+       ("r-graph" ,r-graph)
+       ("r-idr" ,r-idr)
        ("r-iranges" ,r-iranges)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-annotationdbi" ,r-annotationdbi)
        ("r-limma" ,r-limma)
+       ("r-matrixstats" ,r-matrixstats)
        ("r-multtest" ,r-multtest)
        ("r-rbgl" ,r-rbgl)
-       ("r-graph" ,r-graph)
        ("r-regioner" ,r-regioner)
-       ("r-dbi" ,r-dbi)
-       ("r-ensembldb" ,r-ensembldb)
-       ("r-biobase" ,r-biobase)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-rtracklayer" ,r-rtracklayer)
        ("r-s4vectors" ,r-s4vectors)
        ("r-seqinr" ,r-seqinr)
-       ("r-idr" ,r-idr)
-       ("r-genomicalignments" ,r-genomicalignments)
        ("r-summarizedexperiment" ,r-summarizedexperiment)
-       ("r-rsamtools" ,r-rsamtools)
        ("r-venndiagram" ,r-venndiagram)))
     (home-page "http://bioconductor.org/packages/ChIPpeakAnno")
     (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
@@ -2234,14 +2236,14 @@ 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
@@ -2270,14 +2272,14 @@ 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)
@@ -2310,14 +2312,14 @@ 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
@@ -2341,14 +2343,14 @@ 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)))
@@ -2362,18 +2364,19 @@ 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")
@@ -2387,14 +2390,14 @@ 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)
@@ -2421,14 +2424,14 @@ 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)
@@ -2470,14 +2473,14 @@ 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)
@@ -2514,14 +2517,14 @@ 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)
@@ -2553,14 +2556,14 @@ 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
@@ -2612,14 +2615,14 @@ 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
@@ -2684,14 +2687,14 @@ 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)
@@ -2708,14 +2711,14 @@ 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
@@ -2748,14 +2751,14 @@ 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
@@ -2773,14 +2776,14 @@ information about samples and features can be added to the plot.")
 (define-public r-gosemsim
   (package
     (name "r-gosemsim")
-    (version "2.8.0")
+    (version "2.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GOSemSim" version))
        (sha256
         (base32
-         "0ckihpy8jmgn2np1avprz76v9z7i5hqm2gj514c6dmmq3csbc7ib"))))
+         "035jbm14rb1rjp2n00dp5bm88ad8a9afv4lvzpkv39nil98nzbdg"))))
     (properties `((upstream-name . "GOSemSim")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2800,14 +2803,14 @@ sets of GO terms, gene products and gene clusters.")
 (define-public r-anota
   (package
     (name "r-anota")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "anota" version))
        (sha256
         (base32
-         "182fp6dpws516y0igvwn6936higfqvy25haa0xs273f8aczr9cf0"))))
+         "0jchhyf9gqyj0k0fn5zp319griy32cckqpldq9x58z69l2ix2s2c"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-multtest" ,r-multtest)
@@ -2831,14 +2834,14 @@ the data set is suitable for such analysis.")
 (define-public r-sigpathway
   (package
     (name "r-sigpathway")
-    (version "1.50.0")
+    (version "1.52.0")
     (source
       (origin
         (method url-fetch)
         (uri (bioconductor-uri "sigPathway" version))
         (sha256
           (base32
-            "0pygrla2q2151981gshzv51jnj60h1df3vby5gsxqvxn2pdr4bv3"))))
+            "1mc4lb78rcmpihzjiy4w738cbalw5zxms30z8kyy12s6vbxi6hx7"))))
     (properties `((upstream-name . "sigPathway")))
     (build-system r-build-system)
     (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
@@ -2853,17 +2856,18 @@ phenotype of interest.")
 (define-public r-fgsea
   (package
     (name "r-fgsea")
-    (version "1.8.0")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "fgsea" version))
        (sha256
         (base32
-         "0cxxvlmg340l5l5fz4abbwppiri0ibg4navvq5k3wg511mz8ma2q"))))
+         "07mvv1i690q80fm8sxgdqxchamn76409vn91ppgcck2xpi6b8q6c"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocparallel" ,r-biocparallel)
+     `(("r-bh" ,r-bh)
+       ("r-biocparallel" ,r-biocparallel)
        ("r-data-table" ,r-data-table)
        ("r-fastmatch" ,r-fastmatch)
        ("r-ggplot2" ,r-ggplot2)
@@ -2882,14 +2886,14 @@ to multiple hypothesis correction.")
 (define-public r-dose
   (package
     (name "r-dose")
-    (version "3.8.2")
+    (version "3.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DOSE" version))
        (sha256
         (base32
-         "1gh7dhvfc71kawxcfx8xqlir7mwvg5mmz4lqrdrvw5knvi2h3mfa"))))
+         "0dvhnfhzhhzcxm8zhdwrkif7sak4p888sjqfd3a0p77h0hs6g8pv"))))
     (properties `((upstream-name . "DOSE")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2916,14 +2920,14 @@ data.")
 (define-public r-enrichplot
   (package
     (name "r-enrichplot")
-    (version "1.2.0")
+    (version "1.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "enrichplot" version))
        (sha256
         (base32
-         "0cxqfpy6py4k3z3lnlkiwx89r4ymfpdc4hm25dfpazqgjflz5is7"))))
+         "1i9psakvvdc6jn7k7zwpbdhwvf9r8s7649w05mwh1hy978x4rh6h"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
@@ -2952,14 +2956,14 @@ All the visualization methods are developed based on ggplot2 graphics.")
 (define-public r-clusterprofiler
   (package
     (name "r-clusterprofiler")
-    (version "3.10.1")
+    (version "3.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "clusterProfiler" version))
        (sha256
         (base32
-         "1v4fh8ll7zk8yhbaa0nq9xvqrb05kyvbpwkqpnjf07s873805rxm"))))
+         "1jw8h6nlcgd86qhqlcgi3icylb7amcqimlvzg29gay3bf3grwfhq"))))
     (properties
      `((upstream-name . "clusterProfiler")))
     (build-system r-build-system)
@@ -2985,14 +2989,14 @@ profiles (GO and KEGG) of gene and gene clusters.")
 (define-public r-mlinterfaces
   (package
     (name "r-mlinterfaces")
-    (version "1.62.1")
+    (version "1.64.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MLInterfaces" version))
        (sha256
         (base32
-         "1h0x1p2h8x1h276wxx6kcnb4c4s5sglnmd58iigl81a224x8gxwp"))))
+         "0zqvxmvbkig3cc4r5k405s53d7y5ccvrf8kf5j6v8s1kkrklai4j"))))
     (properties `((upstream-name . "MLInterfaces")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3026,14 +3030,14 @@ data in R and Bioconductor containers.")
 (define-public r-annaffy
   (package
     (name "r-annaffy")
-    (version "1.54.0")
+    (version "1.56.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "annaffy" version))
        (sha256
         (base32
-         "16c6allp4vlx0g3nffanrm0mkkf8s2n31dccw4bflnx2pr81bmd5"))))
+         "0sz96lcw0xc4bw1h3x0j40yh5ragmybsq6zwd0adlwzkhvriqjn9"))))
     (build-system r-build-system)
     (arguments
      `(#:phases
@@ -3062,14 +3066,14 @@ It allows searching of biological metadata using various criteria.")
 (define-public r-a4core
   (package
     (name "r-a4core")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "a4Core" version))
        (sha256
         (base32
-         "1d62afxkfp9zbp59ijcn4wd1gdynygw013av41wq8bfm3cx6f9zr"))))
+         "1cr0d1w81iygil3pygqzigfb1a0hc248qd9vqvs0n537cxrxq7i7"))))
     (properties `((upstream-name . "a4Core")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3085,14 +3089,14 @@ arrays.")
 (define-public r-a4classif
   (package
     (name "r-a4classif")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "a4Classif" version))
        (sha256
         (base32
-         "02l77a59865ly3bydv74ff2l2wfb0x5s283g1nx6g1qrw3ly982j"))))
+         "1jif0w3hx020zzwkaza1a26mf34343y7a3v80ic93in6n53yjhj0"))))
     (properties `((upstream-name . "a4Classif")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3113,14 +3117,14 @@ Affymetrix arrays.")
 (define-public r-a4preproc
   (package
     (name "r-a4preproc")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "a4Preproc" version))
        (sha256
         (base32
-         "1dd3fqcc7nr2zbi46k0mnqkh42mfxk894ixfpqg7i9np2523p5gp"))))
+         "13sj4zriq1mian2xcjwkbmmpdjh3h6dgjslar2hc8nmd34cb9xjr"))))
     (properties `((upstream-name . "a4Preproc")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3135,14 +3139,14 @@ is used for preprocessing the arrays.")
 (define-public r-a4reporting
   (package
     (name "r-a4reporting")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "a4Reporting" version))
        (sha256
         (base32
-         "124774z3bfdjgxx2ad40795h92aam21yfx0rw0n01nk2wf6k7xc4"))))
+         "1lail2iw8jmvfdq9brv7i41k6vmbhx2kp21jxq2cj1zva5rcqssj"))))
     (properties `((upstream-name . "a4Reporting")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3158,14 +3162,14 @@ provides reporting features.")
 (define-public r-a4base
   (package
     (name "r-a4base")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "a4Base" version))
        (sha256
         (base32
-         "0k9k3bv99msbwf2y416cz316ssaha2dxvmaddbl7z9037p8mjr70"))))
+         "0yd8gkg3dlkijnms88bxkqsghhc9i32pgd9yaq6hzr67wk879wa1"))))
     (properties `((upstream-name . "a4Base")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3190,14 +3194,14 @@ Affymetrix arrays.")
 (define-public r-a4
   (package
     (name "r-a4")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "a4" version))
        (sha256
         (base32
-         "1iqjy35rqx3m2y0dm2bk4cnzdm1qvbi608bfmrid88w6wmwz3qlk"))))
+         "08146qzsr6mjblmh08g83063nnyrfl35z6p65v71isprkydgxyhy"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-a4base" ,r-a4base)
@@ -3215,14 +3219,14 @@ Affymetrix arrays.")
 (define-public r-abseqr
   (package
     (name "r-abseqr")
-    (version "1.0.0")
+    (version "1.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "abseqR" version))
        (sha256
         (base32
-         "0w0ngxnilcrxlixsz7ls3zm99gyabxwn7w1r3r45n96d4aj075ry"))))
+         "0cbjm7cxjfrkwqhcrrh93w0zf3skmi2p9hyx7acg0ym5fz0ic51r"))))
     (properties `((upstream-name . "abseqR")))
     (build-system r-build-system)
     (inputs
@@ -3261,14 +3265,14 @@ further downstream analysis on its output.")
 (define-public r-bacon
   (package
     (name "r-bacon")
-    (version "1.10.1")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bacon" version))
        (sha256
         (base32
-         "1pd3p1cfggiy08458vplsy3s1zm5jqqcwrv4fks8ra2kf97j38df"))))
+         "1p6h348kwbsan6dwviclwxx02jcdmf580g5f95w2sgn4jnfv7q1q"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biocparallel" ,r-biocparallel)
@@ -3286,14 +3290,14 @@ fitting a three-component normal mixture on z-scores.")
 (define-public r-rgadem
   (package
     (name "r-rgadem")
-    (version "2.30.0")
+    (version "2.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "rGADEM" version))
        (sha256
         (base32
-         "1a3mvxabp7yb275cv1wr0rzyvjhnsaysk2hnmll4z4cci171z2j2"))))
+         "1zf8ayllf1i79wc39vyln2hii1bgg88sw6h1hngkqx4phyvl9q18"))))
     (properties `((upstream-name . "rGADEM")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3311,14 +3315,14 @@ genomic sequence data.")
 (define-public r-motiv
   (package
     (name "r-motiv")
-    (version "1.38.0")
+    (version "1.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MotIV" version))
        (sha256
         (base32
-         "1qrpydwc5bn8f0843qkyhw6920xk8kvq452ird0ij96g6faiv9a8"))))
+         "088z3vyx5h2c4ll4sway01cd4h0x2ayhbv55f6l2kss71v6k6byf"))))
     (properties `((upstream-name . "MotIV")))
     (build-system r-build-system)
     (inputs
@@ -3342,20 +3346,20 @@ distributions, modules and filter motifs.")
 (define-public r-motifstack
   (package
     (name "r-motifstack")
-    (version "1.26.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "motifStack" version))
        (sha256
         (base32
-         "1c4w39ilc4ca4wgi1b6iypadkbxvqjw7k2br0d7q03niw9qjkhxf"))))
+         "0qbv5pvn1g9xfn221vqjmp9vfxpkda1wxkn0kyn2nqyb80d4jf9f"))))
     (properties `((upstream-name . "motifStack")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-ade4" ,r-ade4)
        ("r-biostrings" ,r-biostrings)
-       ("r-grimport" ,r-grimport)
+       ("r-grimport2" ,r-grimport2)
        ("r-htmlwidgets" ,r-htmlwidgets)
        ("r-motiv" ,r-motiv)
        ("r-scales" ,r-scales)
@@ -3373,14 +3377,14 @@ type and symbol colors.")
 (define-public r-genomicscores
   (package
     (name "r-genomicscores")
-    (version "1.6.0")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GenomicScores" version))
        (sha256
         (base32
-         "0lrhkcblvnki6kncwpavs01gbcz22yza6ma8zvfmbrrkfaxqzh8n"))))
+         "17bd61icfycc61b5dij1968h026w7vfd9miwdcbppak1j6s08idq"))))
     (properties `((upstream-name . "GenomicScores")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3404,14 +3408,14 @@ position-specific scores within R and Bioconductor.")
 (define-public r-atacseqqc
   (package
     (name "r-atacseqqc")
-    (version "1.6.4")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ATACseqQC" version))
        (sha256
         (base32
-         "1rblvqar11fib6ip2hq0756vqi6qmncf90jw6i5p5lrgzmaxy8hn"))))
+         "03f130vcd6hd3fv2pg60id0ddd6qkwsyx73gm907xaayf42ar2pj"))))
     (properties `((upstream-name . "ATACseqQC")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3419,6 +3423,7 @@ position-specific scores within R and Bioconductor.")
        ("r-biostrings" ,r-biostrings)
        ("r-bsgenome" ,r-bsgenome)
        ("r-chippeakanno" ,r-chippeakanno)
+       ("r-edger" ,r-edger)
        ("r-genomeinfodb" ,r-genomeinfodb)
        ("r-genomicalignments" ,r-genomicalignments)
        ("r-genomicranges" ,r-genomicranges)
@@ -3448,14 +3453,14 @@ footprints.")
 (define-public r-gofuncr
   (package
     (name "r-gofuncr")
-    (version "1.2.0")
+    (version "1.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GOfuncR" version))
        (sha256
         (base32
-         "021kgcbm8n2yalhzab11cyppwznlkglynnh45wsgy9i2vi2n2znk"))))
+         "1znnkh96yyv6rkbjxx2942nixw4ixdll1f72v92wzsxdcbwkgqdm"))))
     (properties `((upstream-name . "GOfuncR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3495,14 +3500,14 @@ annotations and ontologies.")
 (define-public r-abaenrichment
   (package
     (name "r-abaenrichment")
-    (version "1.12.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ABAEnrichment" version))
        (sha256
         (base32
-         "0bvanqmg1smyckh16m2qn7d68zq4j7n74sgsnbgms5jngbp9158v"))))
+         "0av1dysk7qa8c4a0pp7yq89k8c4y40d2gyvsb8f27slvv2i3aad2"))))
     (properties `((upstream-name . "ABAEnrichment")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3525,14 +3530,14 @@ the brain using an ontology, both provided by the Allen Brain Atlas project.")
 (define-public r-annotationfuncs
   (package
     (name "r-annotationfuncs")
-    (version "1.32.0")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AnnotationFuncs" version))
        (sha256
         (base32
-         "1x11mfabh7kbp39y5rkmrpjkaawx7ab5anfmciamrmrcw1kddbss"))))
+         "12vh07x8s9y74h65q1pnjlma752pz29bmyyhlnqaiy83gsg26hm3"))))
     (properties
      `((upstream-name . "AnnotationFuncs")))
     (build-system r-build-system)
@@ -3550,14 +3555,14 @@ different identifieres using the Biocore Data Team data-packages (e.g.
 (define-public r-annotationtools
   (package
     (name "r-annotationtools")
-    (version "1.56.0")
+    (version "1.58.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "annotationTools" version))
        (sha256
         (base32
-         "0hqy0mq6pkn05p2dv4pw24p697yvikhdn351adf2ynldy6f3sl9z"))))
+         "148fi8bv1m0y81psm0jv1nqvjhvr461drnl0krqd7skcf0mb0fc1"))))
     (properties
      `((upstream-name . "annotationTools")))
     (build-system r-build-system)
@@ -3575,14 +3580,14 @@ text files).")
 (define-public r-allelicimbalance
   (package
     (name "r-allelicimbalance")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AllelicImbalance" version))
        (sha256
         (base32
-         "03524lj6aw9cskbpxzjmi9g708x6p94mf26yz4j941g1d0mc3z91"))))
+         "1f51y8zjgz0wdd33qbs1gpnadbprixr4wcfvff6v3s09rmnr8fng"))))
     (properties
      `((upstream-name . "AllelicImbalance")))
     (build-system r-build-system)
@@ -3616,14 +3621,14 @@ investigation using RNA-seq data.")
 (define-public r-aucell
   (package
     (name "r-aucell")
-    (version "1.4.1")
+    (version "1.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AUCell" version))
        (sha256
         (base32
-         "1kdrs0521cyb8wlc4i3idfprrcy2f9w6kl56hfa94n0brmx62ya9"))))
+         "025q1as9pifbxa7hidlz634q6d7l73zx8mqy4rjbfrk7d5615xvm"))))
     (properties `((upstream-name . "AUCell")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3651,14 +3656,14 @@ needed.")
 (define-public r-ebimage
   (package
     (name "r-ebimage")
-    (version "4.24.0")
+    (version "4.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "EBImage" version))
        (sha256
         (base32
-         "18v2zr7xh0d0xbs7mxa2b6xjqlqiml0hji27gq1351xp5bf2pxvx"))))
+         "0c8rfi40959rbpbizpiizkq21az3lfwf2azlj55yz5m61qp7mgsq"))))
     (properties `((upstream-name . "EBImage")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3690,14 +3695,14 @@ visualization with image data.")
 (define-public r-yamss
   (package
     (name "r-yamss")
-    (version "1.8.1")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "yamss" version))
        (sha256
         (base32
-         "13pln09j08fjsr7bj17apy4j0sr79n7jzshi8jbnz57jil7k6ia9"))))
+         "00756szrmfm1jdayl90jgblydn6sick9nagdf77pn7wzh6wlaj23"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)
@@ -3722,14 +3727,14 @@ analysis.")
 (define-public r-gtrellis
   (package
     (name "r-gtrellis")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gtrellis" version))
        (sha256
         (base32
-         "17c43vs6m6hj90x5is0pbcpcv59gg9z98c47hnvlypgcqch38h6v"))))
+         "00d5swg3brnx8ryzpg7hp3mg9hx3vz4yd1lv2chlp2pj2rhsir1y"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-circlize" ,r-circlize)
@@ -3749,14 +3754,14 @@ genomic categories and to add self-defined graphics in the plot.")
 (define-public r-somaticsignatures
   (package
     (name "r-somaticsignatures")
-    (version "2.18.0")
+    (version "2.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "SomaticSignatures" version))
        (sha256
         (base32
-         "013dslbyq55a41d3n842brjk2bq1kxw0r18mb6drgbxx2sflzc02"))))
+         "0wc4ddwngvkc9jhihzaxx8yazqncl1kbgkx8vqn5gd4w2hx0h5bx"))))
     (properties
      `((upstream-name . "SomaticSignatures")))
     (build-system r-build-system)
@@ -3786,14 +3791,14 @@ decomposition algorithms.")
 (define-public r-yapsa
   (package
     (name "r-yapsa")
-    (version "1.8.0")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "YAPSA" version))
        (sha256
         (base32
-         "1agacimdd1m5yja2xbcsb83mns4svpxbjcsfrvm9ydqdj737i10j"))))
+         "0rfjn2x6hsqiigd53bnl7z5ix5s2mbpr9glsyihsa7i6iazh3n1q"))))
     (properties `((upstream-name . "YAPSA")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3826,14 +3831,14 @@ provided.")
 (define-public r-gcrma
   (package
     (name "r-gcrma")
-    (version "2.54.0")
+    (version "2.56.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gcrma" version))
        (sha256
         (base32
-         "1v5fi98gdmj002ryq0rgsg2l4x3m3w5pz4h3bx4v8lk15azafgim"))))
+         "1wazr3f4hwzpd0cjs2nlnzifr2g1r8a692pxap9xnmrw66zq94s4"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-affy" ,r-affy)
@@ -3862,14 +3867,14 @@ gene-specific bidning is expected.")
 (define-public r-simpleaffy
   (package
     (name "r-simpleaffy")
-    (version "2.58.0")
+    (version "2.60.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "simpleaffy" version))
        (sha256
         (base32
-         "0bry0d2vw0w2rrpnmfm1kl5v4rdclypmy33jvs9l43vd6vx2ra9s"))))
+         "0zjpbjkk27w56mrxsxynkqc298xxsarsnzbd7injg6zakhlmhy6a"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-affy" ,r-affy)
@@ -3890,14 +3895,14 @@ generating high resolution journal figures.")
 (define-public r-yaqcaffy
   (package
     (name "r-yaqcaffy")
-    (version "1.42.0")
+    (version "1.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "yaqcaffy" version))
        (sha256
         (base32
-         "192n1zvd54nm9q71vyb6dcr7ia6givf4bjwf6542jjig085lwhxk"))))
+         "1v12mbai6gf7wpxbyz4clvr7w1mlbv3scjf4kydfin8wwrrzq670"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-simpleaffy" ,r-simpleaffy)))
@@ -3912,14 +3917,14 @@ chips with the MAQC reference datasets.")
 (define-public r-quantro
   (package
     (name "r-quantro")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "quantro" version))
        (sha256
         (base32
-         "1777gjgn855f04yv7hx70h9l8idmjzamkpazaq2cdr8qzhxwy2ib"))))
+         "0zfb2s410ijp0didapnq7q4gn2d26wy785cygxyvg8sq6mlw2cab"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biobase" ,r-biobase)
@@ -3943,14 +3948,14 @@ groups.")
 (define-public r-yarn
   (package
     (name "r-yarn")
-    (version "1.8.1")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "yarn" version))
        (sha256
         (base32
-         "0c84x1zq34hadpsyaa873r8kg0jcxp09c2z63377hlmhsll90l7s"))))
+         "00gmwylpdmssz8xpd91d8fsiyglr7f9vc9bdalpa7w5vg4c6d2f6"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biobase" ,r-biobase)
@@ -3978,14 +3983,14 @@ large RNA-seq experiments.")
 (define-public r-roar
   (package
     (name "r-roar")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "roar" version))
        (sha256
         (base32
-         "15650s9vs7dvmqpvrs4xwn6j4kh14yqsx4daqyhhxxr68kn8mklw"))))
+         "11ib5vr2vrrqsqcikph528c56bp52myyfdlwkklp8m0r15kwpxr7"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)
@@ -4007,14 +4012,14 @@ sites and alignments obtained from standard RNA-seq experiments.")
 (define-public r-xbseq
   (package
     (name "r-xbseq")
-    (version "1.14.1")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "XBSeq" version))
        (sha256
         (base32
-         "0na0jiqfy40bzl243gqc2214k4hibv6v4ndiqwq0c5f78cyr6lph"))))
+         "12l5qnkg6iahwyfmcsf18hys2i9cjn486sacvsqqfcjj3m88w1gy"))))
     (properties `((upstream-name . "XBSeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4044,14 +4049,14 @@ genes.")
 (define-public r-massspecwavelet
   (package
     (name "r-massspecwavelet")
-    (version "1.48.1")
+    (version "1.50.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MassSpecWavelet" version))
        (sha256
         (base32
-         "1xcr568a36b570rldy27wq4a2jn7yf5f6fddlzgx6x944jdn3ckz"))))
+         "1qg73qv69fvf2al7znkh9lmyx5qmkqv2mpl33lahdwzkm0lh6n72"))))
     (properties
      `((upstream-name . "MassSpecWavelet")))
     (build-system r-build-system)
@@ -4068,14 +4073,14 @@ based on @dfn{Continuous Wavelet Transform} (CWT).")
 (define-public r-xcms
   (package
     (name "r-xcms")
-    (version "3.4.4")
+    (version "3.6.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "xcms" version))
        (sha256
         (base32
-         "073f25m7y8z4560k93d99fv72pr7nrgrp054zssi7jhas4l3ddww"))))
+         "06vhqvvzlkc5bslswagrapmn5ag3x84xg9gxk0fhlmgwapqwki1g"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biobase" ,r-biobase)
@@ -4104,14 +4109,14 @@ data for high-throughput, untargeted analyte profiling.")
 (define-public r-wrench
   (package
     (name "r-wrench")
-    (version "1.0.0")
+    (version "1.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Wrench" version))
        (sha256
         (base32
-         "12gfdj2p52pah67bimz14xcwmcb4c2snjwswj0fns7v3v1h9rlqg"))))
+         "1js4dsgpgwq552r4ay78awd5vhzlmva0v8xvn3dy9v18y4j9k94i"))))
     (properties `((upstream-name . "Wrench")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4128,14 +4133,14 @@ that arising from 16s metagenomic surveys.")
 (define-public r-wiggleplotr
   (package
     (name "r-wiggleplotr")
-    (version "1.6.1")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "wiggleplotr" version))
        (sha256
         (base32
-         "12fhbskkjwv4d9bdy3gab8n9pcf7qpwiwgx0248as445vfw8dil3"))))
+         "0yl3ymsk5iijbypjg7lf6mkjgb54893vml2v5aqp2q4l8q0ld7l0"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-assertthat" ,r-assertthat)
@@ -4160,14 +4165,14 @@ visualization of exonic read coverage.")
 (define-public r-widgettools
   (package
     (name "r-widgettools")
-    (version "1.60.0")
+    (version "1.62.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "widgetTools" version))
        (sha256
         (base32
-         "0mz69pdr6q69avsvs6r5ncdkdmgwfislpil4v18dsflw4j454gwf"))))
+         "021b4s5vcy68p95p8rrcz8a8b1gyk4k8zq06snn32k2dqr91xi1a"))))
     (properties `((upstream-name . "widgetTools")))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/widgetTools/")
@@ -4181,14 +4186,14 @@ widgets in R.")
 (define-public r-webbioc
   (package
     (name "r-webbioc")
-    (version "1.54.0")
+    (version "1.56.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "webbioc" version))
        (sha256
         (base32
-         "16n6wc9q51wfpmh9y77p53sqdqdd8pn50c67vf6h4n7gv5wgnpwi"))))
+         "0ilrwzbk0v41p6hwng7jmr3hwwb4skdcjqml1mc3xmh99lcvw8hz"))))
     (build-system r-build-system)
     (inputs
      `(("netpbm" ,netpbm)
@@ -4214,14 +4219,14 @@ Currently only Affymetrix oligonucleotide analysis is supported.")
 (define-public r-zfpkm
   (package
     (name "r-zfpkm")
-    (version "1.4.1")
+    (version "1.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "zFPKM" version))
        (sha256
         (base32
-         "0rvfrjxxvfng9fxxn316gm96v4rahx62vlk3axr2bzjbi1r4s8v5"))))
+         "14knxp8cjjp9fhc6py66c7hrckf112jamz3gl1v60l1f2l1hmfvz"))))
     (properties `((upstream-name . "zFPKM")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4241,14 +4246,14 @@ This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
 (define-public r-rbowtie2
   (package
     (name "r-rbowtie2")
-    (version "1.4.0")
+    (version "1.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rbowtie2" version))
        (sha256
         (base32
-         "045cmfwqzcj4zn6r16hkpmr5sd5y0mxvrs5yynf460fdz2p418cr"))))
+         "1yphnrk5j52gzvy9g6mw05dzh9sm8xxvhyja59ak68nrs1bh3lq4"))))
     (properties `((upstream-name . "Rbowtie2")))
     (build-system r-build-system)
     (inputs
@@ -4264,14 +4269,14 @@ rapid adapter trimming, identification, and read merging.")
 (define-public r-progeny
   (package
     (name "r-progeny")
-    (version "1.4.1")
+    (version "1.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "progeny" version))
        (sha256
         (base32
-         "02z09rbzi305jrwzai8zayxi82563lxcaldp4r9pw564qkbl7pk7"))))
+         "03rm90vfb9ivxhapvs3h5yggfazf8bf5vh1krknvb3xyw27br9dw"))))
     (build-system r-build-system)
     (propagated-inputs `(("r-biobase" ,r-biobase)))
     (home-page "https://github.com/saezlab/progeny")
@@ -4286,14 +4291,14 @@ expression\".")
 (define-public r-arrmnormalization
   (package
     (name "r-arrmnormalization")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ARRmNormalization" version))
        (sha256
         (base32
-         "09wfd4vqfvmkpqn9dwqly1dz4h1ckh621jbwj1dab6q4z0dfmzmd"))))
+         "05m7hy1qd4lr1ylb0ld30dirdl9jfp1zhvifl6wvj40x74b6h2d1"))))
     (properties
      `((upstream-name . "ARRmNormalization")))
     (build-system r-build-system)
@@ -4335,3 +4340,211 @@ 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)))
+
+(define-public r-iclusterplus
+  (package
+    (name "r-iclusterplus")
+    (version "1.20.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "iClusterPlus" version))
+       (sha256
+        (base32
+         "14x43jjhbp4zwb4dv9rwrm5l5p7h76bc1zkdbiikqip9bzph0viq"))))
+    (properties `((upstream-name . "iClusterPlus")))
+    (build-system r-build-system)
+    (native-inputs `(("gfortran" ,gfortran)))
+    (home-page "https://bioconductor.org/packages/iClusterPlus/")
+    (synopsis "Integrative clustering of multi-type genomic data")
+    (description
+     "iClusterPlus is developed for integrative clustering analysis of
+multi-type genomic data and is an enhanced version of iCluster proposed and
+developed by Shen, Olshen and Ladanyi (2009).  Multi-type genomic data arise
+from the experiments where biological samples (e.g. tumor samples) are
+analyzed by multiple techniques, for instance, @dfn{array comparative genomic
+hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so
+on.  In the iClusterPlus model, binary observations such as somatic mutation
+are modeled as Binomial processes; categorical observations such as copy
+number states are realizations of Multinomial random variables; counts are
+modeled as Poisson random processes; and continuous measures are modeled by
+Gaussian distributions.")
+    (license license:gpl2+)))
+
+(define-public r-rbowtie
+  (package
+    (name "r-rbowtie")
+    (version "1.24.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "Rbowtie" version))
+       (sha256
+        (base32
+         "1p8gbd2zn677lq8d009p2cplg1jm2jhn81lppipj638i9ynjh44f"))))
+    (properties `((upstream-name . "Rbowtie")))
+    (build-system r-build-system)
+    (inputs
+     `(("zlib" ,zlib)))
+    (home-page "https://bioconductor.org/packages/Rbowtie/")
+    (synopsis "R bowtie wrapper")
+    (description
+     "This package provides an R wrapper around the popular bowtie short read
+aligner and around SpliceMap, a de novo splice junction discovery and
+alignment tool.")
+    (license license:artistic2.0)))
+
+(define-public r-sgseq
+  (package
+    (name "r-sgseq")
+    (version "1.18.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "SGSeq" version))
+       (sha256
+        (base32
+         "09c0hv74pl310wahyyp4x50g6sz30bvrg24p2j9h7glla5dh2z4s"))))
+    (properties `((upstream-name . "SGSeq")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biostrings" ,r-biostrings)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicalignments" ,r-genomicalignments)
+       ("r-genomicfeatures" ,r-genomicfeatures)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-igraph" ,r-igraph)
+       ("r-iranges" ,r-iranges)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-runit" ,r-runit)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+    (home-page "https://bioconductor.org/packages/SGSeq/")
+    (synopsis "Splice event prediction and quantification from RNA-seq data")
+    (description
+     "SGSeq is a package for analyzing splice events from RNA-seq data.  Input
+data are RNA-seq reads mapped to a reference genome in BAM format.  Genes are
+represented as a splice graph, which can be obtained from existing annotation
+or predicted from the mapped sequence reads.  Splice events are identified
+from the graph and are quantified locally using structurally compatible reads
+at the start or end of each splice variant.  The software includes functions
+for splice event prediction, quantification, visualization and
+interpretation.")
+    (license license:artistic2.0)))
+
+(define-public r-rhisat2
+  (package
+    (name "r-rhisat2")
+    (version "1.0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "Rhisat2" version))
+       (sha256
+        (base32
+         "01jhj5vvfl4n2d0nl3nd1iw9nii85mgw2adnrmxb8wwlxgy240vr"))))
+    (properties `((upstream-name . "Rhisat2")))
+    (build-system r-build-system)
+    (native-inputs
+     `(("which" ,which)))
+    (propagated-inputs
+     `(("r-genomicfeatures" ,r-genomicfeatures)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-sgseq" ,r-sgseq)))
+    (home-page "https://github.com/fmicompbio/Rhisat2")
+    (synopsis "R Wrapper for HISAT2 sequence aligner")
+    (description
+     "This package provides an R interface to the HISAT2 spliced short-read
+aligner by Kim et al. (2015).  The package contains wrapper functions to
+create a genome index and to perform the read alignment to the generated
+index.")
+    (license license:gpl3)))
+
+(define-public r-quasr
+  (package
+    (name "r-quasr")
+    (version "1.24.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "QuasR" version))
+       (sha256
+        (base32
+         "02mdg3mq99gsqq181j3sfh9pid5l7dqjl68rk4fpc1rvm128y743"))))
+    (properties `((upstream-name . "QuasR")))
+    (build-system r-build-system)
+    (inputs
+     `(("zlib" ,zlib)))
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocmanager" ,r-biocmanager)
+       ("r-biocparallel" ,r-biocparallel)
+       ("r-biostrings" ,r-biostrings)
+       ("r-bsgenome" ,r-bsgenome)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicalignments" ,r-genomicalignments)
+       ("r-genomicfeatures" ,r-genomicfeatures)
+       ("r-genomicfiles" ,r-genomicfiles)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-rbowtie" ,r-rbowtie)
+       ("r-rhisat2" ,r-rhisat2)
+       ("r-rhtslib" ,r-rhtslib)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-shortread" ,r-shortread)))
+    (home-page "https://bioconductor.org/packages/QuasR/")
+    (synopsis "Quantify and annotate short reads in R")
+    (description
+     "This package provides a framework for the quantification and analysis of
+short genomic reads.  It covers a complete workflow starting from raw sequence
+reads, over creation of alignments and quality control plots, to the
+quantification of genomic regions of interest.")
+    (license license:gpl2)))
+
+(define-public r-rqc
+  (package
+    (name "r-rqc")
+    (version "1.18.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "Rqc" version))
+       (sha256
+        (base32
+         "09kyn5nc2fqfdm3q07h0x2jyh24vsq5sxxm63ir1lvv250lmal4g"))))
+    (properties `((upstream-name . "Rqc")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocparallel" ,r-biocparallel)
+       ("r-biocstyle" ,r-biocstyle)
+       ("r-biostrings" ,r-biostrings)
+       ("r-biovizbase" ,r-biovizbase)
+       ("r-genomicalignments" ,r-genomicalignments)
+       ("r-genomicfiles" ,r-genomicfiles)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-iranges" ,r-iranges)
+       ("r-knitr" ,r-knitr)
+       ("r-markdown" ,r-markdown)
+       ("r-plyr" ,r-plyr)
+       ("r-rcpp" ,r-rcpp)
+       ("r-reshape2" ,r-reshape2)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-shiny" ,r-shiny)
+       ("r-shortread" ,r-shortread)))
+    (home-page "https://github.com/labbcb/Rqc")
+    (synopsis "Quality control tool for high-throughput sequencing data")
+    (description
+     "Rqc is an optimized tool designed for quality control and assessment of
+high-throughput sequencing data.  It performs parallel processing of entire
+files and produces a report which contains a set of high-resolution
+graphics.")
+    (license license:gpl2+)))