gnu: r-xbseq: Update to 1.16.0.

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

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 4b46edf..a7afd55 100644 (file)
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3137,14 +3137,14 @@ 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
@@ -3160,14 +3160,14 @@ 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
@@ -3192,14 +3192,14 @@ 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)
@@ -3217,14 +3217,14 @@ 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
@@ -3263,14 +3263,14 @@ 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)
@@ -3288,14 +3288,14 @@ fitting a three-component normal mixture on z-scores.")
 (define-public r-rgadem
   (package
     (name "r-rgadem")
-    (version "2.30.0")
+    (version "2.31.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "rGADEM" version))
        (sha256
         (base32
-         "1a3mvxabp7yb275cv1wr0rzyvjhnsaysk2hnmll4z4cci171z2j2"))))
+         "0mck3dsxzjxszfs1cl96kd83q7n85p3763s0y3gwws69jn7p6w5j"))))
     (properties `((upstream-name . "rGADEM")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3313,14 +3313,14 @@ 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
@@ -3344,20 +3344,20 @@ 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)
@@ -3375,14 +3375,14 @@ 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
@@ -3406,14 +3406,14 @@ 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
@@ -3421,6 +3421,7 @@ 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)
@@ -3450,14 +3451,14 @@ 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
@@ -3497,14 +3498,14 @@ 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
@@ -3527,14 +3528,14 @@ 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)
@@ -3552,14 +3553,14 @@ 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)
@@ -3577,14 +3578,14 @@ 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)
@@ -3618,14 +3619,14 @@ 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
@@ -3653,14 +3654,14 @@ 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
@@ -3692,14 +3693,14 @@ 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)
@@ -3724,14 +3725,14 @@ 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)
@@ -3751,14 +3752,14 @@ 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)
@@ -3788,14 +3789,14 @@ 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
@@ -3828,14 +3829,14 @@ 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)
@@ -3864,14 +3865,14 @@ 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)
@@ -3892,14 +3893,14 @@ 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)))
@@ -3914,14 +3915,14 @@ 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)
@@ -3945,14 +3946,14 @@ 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)
@@ -3980,14 +3981,14 @@ 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)
@@ -4009,14 +4010,14 @@ 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