gnu: r-genomicalignments: Update to 1.20.0.

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

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b994104..6db0166 100644 (file)
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7449,13 +7449,13 @@ names in their natural, rather than lexicographic, order.")
 (define-public r-edger
   (package
     (name "r-edger")
-    (version "3.24.3")
+    (version "3.26.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "edgeR" version))
               (sha256
                (base32
-                "15yimsbsxmxhlsfmgw5j7fd8qn08zz4xqxrir1c6n2dc103y22xg"))))
+                "10zhnybcwacgwcdp5p792njzl4kcafvnnnxbd7mszhxrm1sliqr8"))))
     (properties `((upstream-name . "edgeR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7477,13 +7477,13 @@ CAGE.")
 (define-public r-variantannotation
   (package
     (name "r-variantannotation")
-    (version "1.28.13")
+    (version "1.30.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "VariantAnnotation" version))
               (sha256
                (base32
-                "1a7b0bg579ynpbfh5dk87fdgl62r9cwk4zmrl61m6zil7881p3gh"))))
+                "1sd01yv1hnwc16412ilncrrph4gxsr9ds0nqg1czl69fqaixjn1i"))))
     (properties
      `((upstream-name . "VariantAnnotation")))
     (inputs
@@ -7500,6 +7500,7 @@ CAGE.")
        ("r-genomicranges" ,r-genomicranges)
        ("r-iranges" ,r-iranges)
        ("r-summarizedexperiment" ,r-summarizedexperiment)
+       ("r-rhtslib" ,r-rhtslib)
        ("r-rsamtools" ,r-rsamtools)
        ("r-rtracklayer" ,r-rtracklayer)
        ("r-s4vectors" ,r-s4vectors)
@@ -7515,13 +7516,13 @@ coding changes and predict coding outcomes.")
 (define-public r-limma
   (package
     (name "r-limma")
-    (version "3.38.3")
+    (version "3.40.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "limma" version))
               (sha256
                (base32
-                "08va8jggmv61wym955mnb1n31mgikrmjys7dl1kp5hp3yia8jg7l"))))
+                "03qxn3bs0gxq480vjd26cvhiq7jisw7kpmb3wpkrjk8jnsb10aax"))))
     (build-system r-build-system)
     (home-page "http://bioinf.wehi.edu.au/limma")
     (synopsis "Package for linear models for microarray and RNA-seq data")
@@ -7534,13 +7535,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.")
 (define-public r-xvector
   (package
     (name "r-xvector")
-    (version "0.22.0")
+    (version "0.24.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "XVector" version))
               (sha256
                (base32
-                "01fph1ydd6g0rl5mcw54spx22glq2kqv7wyw8bqw0plmabzcwwdm"))))
+                "12y09pwy86h1za6cmaxs960r7fs0vjzhl0li8jn59vqq9liza1ap"))))
     (properties
      `((upstream-name . "XVector")))
     (build-system r-build-system)
@@ -7570,13 +7571,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.")
 (define-public r-genomicranges
   (package
     (name "r-genomicranges")
-    (version "1.34.0")
+    (version "1.36.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicRanges" version))
               (sha256
                (base32
-                "0bgh14d15dpf2iy36qinw45r6n45rqkf0ghazrdl3jfva6vbrb29"))))
+                "1285fr8qjd7d0ixpv7d5imi0n6wzc4k6yia1rkmig71qd2gg556k"))))
     (properties
      `((upstream-name . "GenomicRanges")))
     (build-system r-build-system)
@@ -7599,13 +7600,13 @@ manipulating genomic intervals and variables defined along a genome.")
 (define-public r-biobase
   (package
     (name "r-biobase")
-    (version "2.42.0")
+    (version "2.44.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Biobase" version))
               (sha256
                (base32
-                "10nr6nrkj5vlq8hsgbhbhv669z0dbpz4m3vz9k32rx1czbrrqwin"))))
+                "15yl92niqamx3lmwd11zlk0xniibqnh1gi280iadxicmchi83npc"))))
     (properties
      `((upstream-name . "Biobase")))
     (build-system r-build-system)
@@ -7621,13 +7622,13 @@ on Bioconductor or which replace R functions.")
 (define-public r-annotationdbi
   (package
     (name "r-annotationdbi")
-    (version "1.44.0")
+    (version "1.46.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AnnotationDbi" version))
               (sha256
                (base32
-                "1954vimkx5yb9irppq8vssq0f3yjkg36w38b9r0rqmijx1ps7x5d"))))
+                "0lfq5668a6sq4kqhxx78hl3jcaqdsaaliiybl9xyya2scdk8c29c"))))
     (properties
      `((upstream-name . "AnnotationDbi")))
     (build-system r-build-system)
@@ -7648,13 +7649,13 @@ annotation data packages using SQLite data storage.")
 (define-public r-biomart
   (package
     (name "r-biomart")
-    (version "2.38.0")
+    (version "2.40.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "biomaRt" version))
               (sha256
                (base32
-                "1lshkknp7dmr3p6dd2zbv86cc71h53ggh9ji83jcjym8sgbbspl2"))))
+                "1i457s91bn7n60bzw3zk4h64xgmawlrr6bq4z4cb7jlm04hdq8qm"))))
     (properties
      `((upstream-name . "biomaRt")))
     (build-system r-build-system)
@@ -7681,13 +7682,13 @@ powerful online queries from gene annotation to database mining.")
 (define-public r-biocparallel
   (package
     (name "r-biocparallel")
-    (version "1.16.6")
+    (version "1.18.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocParallel" version))
               (sha256
                (base32
-                "1iv2xzm6lz371z0llhcxl8hmc5jfw0hjwnf1qc8d7jk9djgcaks2"))))
+                "0v8rhf3hbgb3v32h2pmsv1y6q2x4airmpp50fk7z6ardcn4aza7x"))))
     (properties
      `((upstream-name . "BiocParallel")))
     (build-system r-build-system)
@@ -7706,13 +7707,13 @@ objects.")
 (define-public r-biostrings
   (package
     (name "r-biostrings")
-    (version "2.50.2")
+    (version "2.52.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Biostrings" version))
               (sha256
                (base32
-                "16cqqc8i6gb0jcz0lizfqqxsq7g0yb0ll2s9qzmb45brp07dg8f7"))))
+                "0inrl97hli3qz6cfxcikc4picmbrqc8phdgqi18ynlvxy5ql64h4"))))
     (properties
      `((upstream-name . "Biostrings")))
     (build-system r-build-system)
@@ -7776,13 +7777,13 @@ tab-delimited (tabix) files.")
 (define-public r-delayedarray
   (package
     (name "r-delayedarray")
-    (version "0.8.0")
+    (version "0.10.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "DelayedArray" version))
               (sha256
                (base32
-                "0cl5anqkjwvqx19snjhz0zj8cp8ibckiifl28h821h50g62nvb2f"))))
+                "0l907ggxndn3f29zvsd5pppmp4c31rb22r6zkhvgph7xdxahyy6z"))))
     (properties
      `((upstream-name . "DelayedArray")))
     (build-system r-build-system)
@@ -7791,6 +7792,7 @@ tab-delimited (tabix) files.")
        ("r-biocparallel" ,r-biocparallel)
        ("r-s4vectors" ,r-s4vectors)
        ("r-iranges" ,r-iranges)
+       ("r-matrix" ,r-matrix)
        ("r-matrixstats" ,r-matrixstats)))
     (home-page "https://bioconductor.org/packages/DelayedArray")
     (synopsis "Delayed operations on array-like objects")
@@ -7807,13 +7809,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns),
 (define-public r-summarizedexperiment
   (package
     (name "r-summarizedexperiment")
-    (version "1.12.0")
+    (version "1.14.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "SummarizedExperiment" version))
               (sha256
                (base32
-                "07805572xhpj5mfwq6kw1ha21wgalqvhh4ydvafyl1bnf3r20vps"))))
+                "1ypk63pdml89y81pr41i2zq0fimsaxsa5lgpg6xs5cwikyaq0pci"))))
     (properties
      `((upstream-name . "SummarizedExperiment")))
     (build-system r-build-system)
@@ -7838,13 +7840,13 @@ samples.")
 (define-public r-genomicalignments
   (package
     (name "r-genomicalignments")
-    (version "1.18.1")
+    (version "1.20.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicAlignments" version))
               (sha256
                (base32
-                "1maslav2r34wjyzh2nlwa862in1ir7i5xk57nw2nlfh5gqy112jd"))))
+                "13zw7bb1adgph9bf9b9y725nr0320b80y70p2yqf3bjb2klfxf55"))))
     (properties
      `((upstream-name . "GenomicAlignments")))
     (build-system r-build-system)