gnu: r-ihw: Update to 1.12.0.

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

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 0fb6b1a..94c2963 100644 (file)
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1545,14 +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
@@ -1572,14 +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
@@ -1596,14 +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)
@@ -1621,14 +1621,14 @@ genes or proteins in these datasets.")
 (define-public r-inspect
   (package
     (name "r-inspect")
-    (version "1.12.2")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "INSPEcT" version))
        (sha256
         (base32
-         "1ykkr15b4bc2carwppf9yxzpl2n6lqpc6z6i2qy37vc6xffzgdx4"))))
+         "1a7smljndiyahgpj6vl079pvi3n0rfk1vkdkp799y4nm2wnhn93r"))))
     (properties `((upstream-name . "INSPEcT")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1663,14 +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
@@ -1690,14 +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
@@ -1716,20 +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")
@@ -1777,21 +1779,20 @@ possible, parallelization is achieved using the BiocParallel framework.")
 (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)
@@ -1812,14 +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
@@ -1838,14 +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
@@ -1876,13 +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)
@@ -1899,14 +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)))
@@ -1950,14 +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/")
@@ -1999,14 +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
@@ -2023,14 +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)
@@ -2053,14 +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