gnu: r-motifrg: Update to 1.24.0.

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

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 98149f2..8a5d9fd 100644 (file)
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2079,7 +2079,7 @@ accurately delineate genomic rearrangements throughout the genome.")
 (define-public diamond
   (package
     (name "diamond")
-    (version "0.9.21")
+    (version "0.9.22")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -2088,7 +2088,7 @@ accurately delineate genomic rearrangements throughout the genome.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "1cf98vcsiwcv3c4apg50w1240v1mpw0zln1sdw3g692dqa4y041z"))))
+                "0adp87r9ak63frdrdmrdfhsn6g0jnnyq1lr2wibvqbxcl37iir9m"))))
     (build-system cmake-build-system)
     (arguments
      '(#:tests? #f ; no "check" target
@@ -3450,6 +3450,42 @@ The main functions of FastQC are:
 @end itemize\n")
     (license license:gpl3+)))
 
+(define-public fastp
+  (package
+    (name "fastp")
+    (version "0.14.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/OpenGene/fastp.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "1r6ms5zbf5rps4rgp4z73nczadl00b5rqylw8f684isfz27dp0xh"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ; there are none
+       #:make-flags
+       (list (string-append "BINDIR=" (assoc-ref %outputs "out") "/bin"))
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (add-before 'install 'create-target-dir
+           (lambda* (#:key outputs #:allow-other-keys)
+             (mkdir-p (string-append (assoc-ref outputs "out") "/bin"))
+             #t)))))
+    (inputs
+     `(("zlib" ,zlib)))
+    (home-page "https://github.com/OpenGene/fastp/")
+    (synopsis "All-in-one FastQ preprocessor")
+    (description
+     "Fastp is a tool designed to provide fast all-in-one preprocessing for
+FastQ files.  This tool has multi-threading support to afford high
+performance.")
+    (license license:expat)))
+
 (define-public htslib
   (package
     (name "htslib")
@@ -6083,20 +6119,20 @@ information as possible.")
 (define-public r-vegan
   (package
     (name "r-vegan")
-    (version "2.5-1")
+    (version "2.5-2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "vegan" version))
        (sha256
         (base32
-         "0pynr02d1xngda6c3va8fc4nxpgfkawhzcnz1ws4dnarp9b1w90r"))))
+         "13pyqvlpz64qibi8k5d109v7q09j06mbv6ndix3n4cn21mjx391c"))))
     (build-system r-build-system)
     (native-inputs
      `(("gfortran" ,gfortran)))
     (propagated-inputs
      `(("r-cluster" ,r-cluster)
-       ("r-knitr" ,r-knitr)
+       ("r-knitr" ,r-knitr) ; needed for vignettes
        ("r-lattice" ,r-lattice)
        ("r-mass" ,r-mass)
        ("r-mgcv" ,r-mgcv)
@@ -6113,14 +6149,14 @@ data types as well.")
 (define-public r-annotate
   (package
     (name "r-annotate")
-    (version "1.56.2")
+    (version "1.58.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "annotate" version))
        (sha256
         (base32
-         "0ybg9k1s289h15nj1kp9821i1rsk1gkn8i8blplmk7gsgpbw1f42"))))
+         "1qmncyvy147a1ll3iri45p822kcs3s7583jfnq9jf6sz9ilk8cjf"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
@@ -6140,13 +6176,13 @@ microarrays.")
 (define-public r-copynumber
   (package
     (name "r-copynumber")
-    (version "1.18.0")
+    (version "1.20.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "copynumber" version))
               (sha256
                (base32
-                "01kcwzl485yjrkgyg8117b1il957ss0v6rq4bbxf4ksd5fzcjmyx"))))
+                "0y9nnwb0psphp3ix88wj2f8z5gr45r5znf55w892ysm27isdpmms"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-s4vectors" ,r-s4vectors)
@@ -6163,14 +6199,14 @@ penalized least squares regression method.")
 (define-public r-geneplotter
   (package
     (name "r-geneplotter")
-    (version "1.56.0")
+    (version "1.58.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "geneplotter" version))
        (sha256
         (base32
-         "1z3g7frc1iviwrsv2dlm4nqvkc0685h4va0388yfxn102ln8wwma"))))
+         "055g28xgiazl4l0gkg8xiamks64f5yckjjyvw1abd6d6qjavwx0g"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotate" ,r-annotate)
@@ -6188,14 +6224,14 @@ penalized least squares regression method.")
 (define-public r-genefilter
   (package
     (name "r-genefilter")
-    (version "1.60.0")
+    (version "1.62.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "genefilter" version))
        (sha256
         (base32
-         "173swlg6gj4kdllbqvyiw5dggbcxiwlwpqmllsv4dxzn7h25i3g7"))))
+         "14l0ff02spmjwxj0m1czhg5vlkgwcfi73cym8m2n9vn6i7bjdaqi"))))
     (build-system r-build-system)
     (native-inputs
      `(("gfortran" ,gfortran)))
@@ -6215,14 +6251,14 @@ high-throughput sequencing experiments.")
 (define-public r-deseq2
   (package
     (name "r-deseq2")
-    (version "1.18.1")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DESeq2" version))
        (sha256
         (base32
-         "1iyimg1s0x5pdmvl8x08s8h0v019y0nhjzs50chagbpk2x91fsmv"))))
+         "1wjnfpb41a9mmf9a22bz4zh7r1d4id50vpdc1mn5vfzrz7li9qik"))))
     (properties `((upstream-name . "DESeq2")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6252,14 +6288,14 @@ distribution.")
 (define-public r-dexseq
   (package
     (name "r-dexseq")
-    (version "1.24.4")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DEXSeq" version))
        (sha256
         (base32
-         "1a80yv742fx5c7qav7imsdybphf0d5bixsqyf8w5zng7fk8j16d5"))))
+         "1mqb3mdxcsi3largsl7k27bvqrgps9ixv806xvmf29pw0xn05sg1"))))
     (properties `((upstream-name . "DEXSeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6295,14 +6331,14 @@ exploration of the results.")
 (define-public r-annotationforge
   (package
     (name "r-annotationforge")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AnnotationForge" version))
        (sha256
         (base32
-         "01vbrf76vqfvxh6vpfxkjwccxggnha3byqzj333glqz2b6kwx5q1"))))
+         "12ffj7h95adiya5mzyjxazqn1qgr434ajpabfcyhrj5v83s4vk65"))))
     (properties
      `((upstream-name . "AnnotationForge")))
     (build-system r-build-system)
@@ -6325,14 +6361,14 @@ databases.  Packages produced are intended to be used with AnnotationDbi.")
 (define-public r-rbgl
   (package
     (name "r-rbgl")
-    (version "1.54.0")
+    (version "1.56.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RBGL" version))
        (sha256
         (base32
-         "18jad23i3899ypv4bg3l47cvvs3qnj1pqis2p9x0135yv5y6wnv7"))))
+         "0hj972mmqpyi5fx1rq33kysavdyz4nspi6gcffzi3rv339m0anhf"))))
     (properties `((upstream-name . "RBGL")))
     (build-system r-build-system)
     (propagated-inputs `(("r-graph" ,r-graph)))
@@ -6346,14 +6382,14 @@ the graph algorithms contained in the Boost library.")
 (define-public r-gseabase
   (package
     (name "r-gseabase")
-    (version "1.40.1")
+    (version "1.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GSEABase" version))
        (sha256
         (base32
-         "10cmjxahg2plwacfan6g0k8cwyzya96ypc7m1r79gwqkyykxw5fz"))))
+         "11bv92svik399q677jv96b71i4bq68xxyxn1yijpdik2lq4hgl7a"))))
     (properties `((upstream-name . "GSEABase")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6373,14 +6409,14 @@ Enrichment Analysis} (GSEA).")
 (define-public r-category
   (package
     (name "r-category")
-    (version "2.44.0")
+    (version "2.46.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Category" version))
        (sha256
         (base32
-         "0mkav04vbla0xfa0dssxdd0rjs589sxi83xklf5iq5hj3dm8y0i8"))))
+         "03wfqa8d1dgwsm327zl2mpkq7dq3mzhq12598qz3ylfhrwplbgx0"))))
     (properties `((upstream-name . "Category")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6404,14 +6440,14 @@ analysis.")
 (define-public r-gostats
   (package
     (name "r-gostats")
-    (version "2.44.0")
+    (version "2.46.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GOstats" version))
        (sha256
         (base32
-         "04gqfdlx9fxf97qf0l28x4aaqvl10n6v58qiz5fiaw05sbj1pf1i"))))
+         "1i5mydz5d95w2k28qr9j01hmbnl2id55jq94jvcpcyp1pvinkdq0"))))
     (properties `((upstream-name . "GOstats")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6435,14 +6471,14 @@ testing and other simple calculations.")
 (define-public r-shortread
   (package
     (name "r-shortread")
-    (version "1.36.1")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ShortRead" version))
        (sha256
         (base32
-         "1cyv47632m9ljkxfsvnvmd19sb607ys5kz8fwh6v39dnw16g0a6m"))))
+         "038z3z7qaw5bpgjzy91sjkybsny6jwjjsrnnq4gdqdw9ss1qy1fb"))))
     (properties `((upstream-name . "ShortRead")))
     (build-system r-build-system)
     (inputs
@@ -6477,14 +6513,14 @@ ungapped alignment formats.")
 (define-public r-systempiper
   (package
     (name "r-systempiper")
-    (version "1.12.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "systemPipeR" version))
        (sha256
         (base32
-         "11mj8pjq5vj25768vmagpzv74fvi3p3kdk5zdlznqyiaggri04cv"))))
+         "1550pd63mmky0vgkmpni7zf14kqz1741wv63nfaw29kcmhh3m5lm"))))
     (properties `((upstream-name . "systemPipeR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6523,14 +6559,14 @@ annotation infrastructure.")
 (define-public r-grohmm
   (package
     (name "r-grohmm")
-    (version "1.12.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "groHMM" version))
        (sha256
         (base32
-         "0cjkj0ypyc4dfi9s8dh88kh6q4xlpnc0wal7njg4b4gqj0l2hva7"))))
+         "1kjb14apyly44qdlx2ld6gr69wlazd4mbhs58l35hir12aphgrzp"))))
     (properties `((upstream-name . "groHMM")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6842,13 +6878,13 @@ barplots or heatmaps.")
 (define-public r-biocgenerics
   (package
     (name "r-biocgenerics")
-    (version "0.24.0")
+    (version "0.26.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocGenerics" version))
               (sha256
                (base32
-                "03wxvhxyrhipbgcg83lqlfn7p9gbzzrnl48y0dq7303xgp232zai"))))
+                "19qxhy2cd3pykkhzbb5q3crgaxf65cpzf2mkfsz16gqhi8flj72p"))))
     (properties
      `((upstream-name . "BiocGenerics")))
     (build-system r-build-system)
@@ -6862,13 +6898,13 @@ packages.")
 (define-public r-biocinstaller
   (package
     (name "r-biocinstaller")
-    (version "1.28.0")
+    (version "1.30.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocInstaller" version))
               (sha256
                (base32
-                "19fga27bv6q9v5mpil74y76lahmnwvpg2h33rdx1r79nvljkd19d"))))
+                "1xg1gi1hf5vflp71ji21gnmr4kcjpx8a6c47cllpc7yqnjv5nfg0"))))
     (properties
      `((upstream-name . "BiocInstaller")))
     (build-system r-build-system)
@@ -6881,13 +6917,13 @@ Bioconductor, CRAN, and Github.")
 (define-public r-biocviews
   (package
     (name "r-biocviews")
-    (version "1.46.0")
+    (version "1.48.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "biocViews" version))
               (sha256
                (base32
-                "09zyqj1kqc089lmh9sliy0acanx9zimcasvp71dsrg2bqm08r1md"))))
+                "1yx2lir67ny0j150wyfqca0wsxp84byri8nscbs9qlndkh2jppq9"))))
     (properties
      `((upstream-name . "biocViews")))
     (build-system r-build-system)
@@ -6932,13 +6968,13 @@ authoring books and technical documents with R Markdown.")
 (define-public r-biocstyle
   (package
    (name "r-biocstyle")
-   (version "2.6.1")
+   (version "2.8.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocStyle" version))
               (sha256
                (base32
-                "03pp04pkcq99kdv2spzr995h2cxsza7l6w3d4gp4112m06prcybm"))))
+                "17m901ylz00w1a3nq5f910v55zixm1nr6rb3qrsbhqd94qzr0l2p"))))
     (properties
      `((upstream-name . "BiocStyle")))
     (build-system r-build-system)
@@ -6957,13 +6993,13 @@ functionality.")
 (define-public r-bioccheck
   (package
     (name "r-bioccheck")
-    (version "1.14.0")
+    (version "1.16.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocCheck" version))
               (sha256
                (base32
-                "1nzp8kgw13z9pgf885rplj6k37jcldfhbz0adqclxr2gq0yalmyx"))))
+                "1srp1g809f1nn0fyqknr7r6dq89bw1xpjvmygr7cw6ffknbc671s"))))
     (properties
      `((upstream-name . "BiocCheck")))
     (build-system r-build-system)
@@ -7048,13 +7084,13 @@ that accept short and long options.")
 (define-public r-dnacopy
   (package
     (name "r-dnacopy")
-    (version "1.52.0")
+    (version "1.54.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "DNAcopy" version))
               (sha256
                (base32
-                "127il5rlg1hzjlhwhs64x3nm18p00q1pd9ckb2b9ifl0rax95wai"))))
+                "03hfhmmc5y60r2gcgm367w2fr7qj115l74m9bp3h9qpn5yci0d8n"))))
     (properties
      `((upstream-name . "DNAcopy")))
     (build-system r-build-system)
@@ -7070,13 +7106,13 @@ abnormal copy number.")
 (define-public r-s4vectors
   (package
     (name "r-s4vectors")
-    (version "0.16.0")
+    (version "0.18.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "S4Vectors" version))
               (sha256
                (base32
-                "03s8vz33nl6mivjb7dbvj702dkypi340lji1sjban03fyyls0hw0"))))
+                "0qvj2j0zl4djjl7vrwc6xak6h8dxr53iwypfbcvfb3sh7jwhdiz5"))))
     (properties
      `((upstream-name . "S4Vectors")))
     (build-system r-build-system)
@@ -7122,13 +7158,13 @@ utilities for sequence data management under the ACNUC system.")
 (define-public r-iranges
   (package
     (name "r-iranges")
-    (version "2.12.0")
+    (version "2.14.10")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "IRanges" version))
               (sha256
                (base32
-                "1vqczb9wlxsmpwpqig6j1dmiblcfpq6mgnq8qwzcrvddm4cp47m5"))))
+                "10ccw930vfmkskkrzbps14xglqlkxf588623dr7f1a9ckx7yr2p6"))))
     (properties
      `((upstream-name . "IRanges")))
     (build-system r-build-system)
@@ -7174,13 +7210,13 @@ ID and species.  It is used by functions in the GenomeInfoDb package.")
 (define-public r-genomeinfodb
   (package
     (name "r-genomeinfodb")
-    (version "1.14.0")
+    (version "1.16.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomeInfoDb" version))
               (sha256
                (base32
-                "1jhm0imkac4gvchbjxj408aakk39xdv2fyh818d3lk295bz6bnyp"))))
+                "0yhnqhaydmmq7ihmhj3rbal4afq5p993l2qqrd0n5wmbyg7glg2d"))))
     (properties
      `((upstream-name . "GenomeInfoDb")))
     (build-system r-build-system)
@@ -7202,13 +7238,13 @@ names in their natural, rather than lexicographic, order.")
 (define-public r-edger
   (package
     (name "r-edger")
-    (version "3.20.9")
+    (version "3.22.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "edgeR" version))
               (sha256
                (base32
-                "0y52snwbz37xzdd7gihdkqczbndlfzmmypv6hri3ymjyfmlx6qaw"))))
+                "07py2g6vg9jbflwhc1hnzr2silbinrjwxq3mkq30nzjgf0n0hrf3"))))
     (properties `((upstream-name . "edgeR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7230,13 +7266,13 @@ CAGE.")
 (define-public r-variantannotation
   (package
     (name "r-variantannotation")
-    (version "1.24.5")
+    (version "1.26.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "VariantAnnotation" version))
               (sha256
                (base32
-                "07ywn3c4w83l3sr76d0z3b1nv9icgdh3phsjlc6cfx7i6nfmvxw2"))))
+                "06bccdf57vja7m63chmgc4539lwng3q3b8zxn285fj8524l6mcn7"))))
     (properties
      `((upstream-name . "VariantAnnotation")))
     (inputs
@@ -7268,13 +7304,13 @@ coding changes and predict coding outcomes.")
 (define-public r-limma
   (package
     (name "r-limma")
-    (version "3.34.9")
+    (version "3.36.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "limma" version))
               (sha256
                (base32
-                "1y2fm61g5i0fn0j3l31xvwh9zww9bpkc4nwzb1d0yv1cag20jkdc"))))
+                "1982g5v35ilfgxm2vkq1p3j1bbir795pjvfzx4nzam2rlqqymbqm"))))
     (build-system r-build-system)
     (home-page "http://bioinf.wehi.edu.au/limma")
     (synopsis "Package for linear models for microarray and RNA-seq data")
@@ -7287,13 +7323,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.")
 (define-public r-xvector
   (package
     (name "r-xvector")
-    (version "0.18.0")
+    (version "0.20.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "XVector" version))
               (sha256
                (base32
-                "1i4i3kdxr78lr1kcxq657p11ybi7kq10c8kyaqyh6gfc8i9rhvmk"))))
+                "1zjlhh9lsyhg0js1858csyw2389kbrzdqnqnha833wazkwxilp3f"))))
     (properties
      `((upstream-name . "XVector")))
     (build-system r-build-system)
@@ -7323,13 +7359,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.")
 (define-public r-genomicranges
   (package
     (name "r-genomicranges")
-    (version "1.30.3")
+    (version "1.32.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicRanges" version))
               (sha256
                (base32
-                "07cszc9ri94nzk4dffwnsj247ih6pchnrzrvnb0q4dkk33gwy8n1"))))
+                "03gmka6rlz18vd4229796l5l3l6446v5cb90sn2nb5knjbp84hni"))))
     (properties
      `((upstream-name . "GenomicRanges")))
     (build-system r-build-system)
@@ -7352,13 +7388,13 @@ manipulating genomic intervals and variables defined along a genome.")
 (define-public r-biobase
   (package
     (name "r-biobase")
-    (version "2.38.0")
+    (version "2.40.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Biobase" version))
               (sha256
                (base32
-                "1cgm1ja1kp56zdlzyy9ggbkfn8r2vbsd4hncmz8g4hjd47fg18kg"))))
+                "1iwds2a5ir29k19dbpynlc7nn836cw2gamchhgpi2jf2xar9m9jz"))))
     (properties
      `((upstream-name . "Biobase")))
     (build-system r-build-system)
@@ -7374,13 +7410,13 @@ on Bioconductor or which replace R functions.")
 (define-public r-annotationdbi
   (package
     (name "r-annotationdbi")
-    (version "1.40.0")
+    (version "1.42.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AnnotationDbi" version))
               (sha256
                (base32
-                "1dh4qs1a757n640gs34lf6z2glc96nan86x0sqaw5csadl2rhnlc"))))
+                "0afkbzli08vq02r2pr9phrz3rxd6ilp1w7yw8y99nbjiz14f8b1c"))))
     (properties
      `((upstream-name . "AnnotationDbi")))
     (build-system r-build-system)
@@ -7401,13 +7437,13 @@ annotation data packages using SQLite data storage.")
 (define-public r-biomart
   (package
     (name "r-biomart")
-    (version "2.34.2")
+    (version "2.36.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "biomaRt" version))
               (sha256
                (base32
-                "1zlgs2zg0lmnk572p55n7m34nkxka8w10x8f2ndssjkffl2csy79"))))
+                "0b70s350ffc74v3xz5c3jpazr9zxdb7gjmjfj7aghlsrizrspill"))))
     (properties
      `((upstream-name . "biomaRt")))
     (build-system r-build-system)
@@ -7434,13 +7470,13 @@ powerful online queries from gene annotation to database mining.")
 (define-public r-biocparallel
   (package
     (name "r-biocparallel")
-    (version "1.12.0")
+    (version "1.14.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocParallel" version))
               (sha256
                (base32
-                "13ng3n2wsgl3fh0v6jnz3vg51k5c1sh44pqdvblcrcd1qyjmmqhd"))))
+                "00qg1kg2l9qqpyjaw5q910cmf84vwfiw1fhsx3ig784gwinwgj6n"))))
     (properties
      `((upstream-name . "BiocParallel")))
     (build-system r-build-system)
@@ -7459,13 +7495,13 @@ objects.")
 (define-public r-biostrings
   (package
     (name "r-biostrings")
-    (version "2.46.0")
+    (version "2.48.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Biostrings" version))
               (sha256
                (base32
-                "0vg50qdlxqcm2d6axjnzg8wh8pr4c5gz03l8bdl0llmwzp0zclzk"))))
+                "118b490jk87ydigm6ln25ms4kskzkw0akmh77clzznhzpqnxsi6j"))))
     (properties
      `((upstream-name . "Biostrings")))
     (build-system r-build-system)
@@ -7485,13 +7521,13 @@ biological sequences or sets of sequences.")
 (define-public r-rsamtools
   (package
     (name "r-rsamtools")
-    (version "1.30.0")
+    (version "1.32.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Rsamtools" version))
               (sha256
                (base32
-                "0pjny5fjvbnfdyhl3bwxin678sha2drvs00sivxh3l772cn6yams"))))
+                "1s65y5wn4d0x8zsljg2kmhcl6r9884h95kr041j7hp49bmxg3an6"))))
     (properties
      `((upstream-name . "Rsamtools")))
     (build-system r-build-system)
@@ -7529,18 +7565,19 @@ files.")
 (define-public r-delayedarray
   (package
     (name "r-delayedarray")
-    (version "0.4.1")
+    (version "0.6.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "DelayedArray" version))
               (sha256
                (base32
-                "0s7h2giyvz04cg6248kbbzpwhxdrpnsvl2s8k5c8ricisd9aaz4b"))))
+                "0n3w57cwy911q812wc8658y0v3xgpmg379sj98kfqdxa80z1mxdf"))))
     (properties
      `((upstream-name . "DelayedArray")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocparallel" ,r-biocparallel)
        ("r-s4vectors" ,r-s4vectors)
        ("r-iranges" ,r-iranges)
        ("r-matrixstats" ,r-matrixstats)))
@@ -7559,13 +7596,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns),
 (define-public r-summarizedexperiment
   (package
     (name "r-summarizedexperiment")
-    (version "1.8.1")
+    (version "1.10.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "SummarizedExperiment" version))
               (sha256
                (base32
-                "19vlwnby83fqjrilsxvnvgz0gvby7mrxvlmx18nb3p1w591ddfjh"))))
+                "0v3zxl9cqsv79ag5cnvzlhvgaz5cr8f4rn7flmwnwpqd508cznl1"))))
     (properties
      `((upstream-name . "SummarizedExperiment")))
     (build-system r-build-system)
@@ -7590,13 +7627,13 @@ samples.")
 (define-public r-genomicalignments
   (package
     (name "r-genomicalignments")
-    (version "1.14.2")
+    (version "1.16.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicAlignments" version))
               (sha256
                (base32
-                "1659nj1xps7vliy5955i51x6hvrf16n1z0dfh10mmpaaswn2d2mv"))))
+                "00pi2cnkkbj2023fg2x2cmglkdalwzy1vr3glsikwz7ix9yylcaw"))))
     (properties
      `((upstream-name . "GenomicAlignments")))
     (build-system r-build-system)
@@ -7623,13 +7660,13 @@ alignments.")
 (define-public r-rtracklayer
   (package
     (name "r-rtracklayer")
-    (version "1.38.3")
+    (version "1.40.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "rtracklayer" version))
               (sha256
                (base32
-                "1khzfczm35k5lq9h0jlqrq01192spzjyh8s6is89spj006flwn4k"))))
+                "0l90jn4df3akxl0n1i9wvnbjqrzjc0d15r8vqr7b15q2117mrn5r"))))
     (build-system r-build-system)
     (arguments
      `(#:phases
@@ -7641,6 +7678,8 @@ alignments.")
              (substitute* "NAMESPACE"
                (("import\\(zlibbioc\\)") ""))
              #t)))))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
     (inputs
      `(("zlib" ,zlib)))
     (propagated-inputs
@@ -7668,13 +7707,13 @@ as well as query and modify the browser state, such as the current viewport.")
 (define-public r-genomicfeatures
   (package
     (name "r-genomicfeatures")
-    (version "1.30.3")
+    (version "1.32.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicFeatures" version))
               (sha256
                (base32
-                "010vn8hlwbnw12pd1d8pv6m12yp3xwx557gba5rbjq9p4qypnn3z"))))
+                "1cqcl72q0k5wylw1brn4g4h7xzys1v06piry19cvp0gjcvm5sp7a"))))
     (properties
      `((upstream-name . "GenomicFeatures")))
     (build-system r-build-system)
@@ -7690,7 +7729,6 @@ as well as query and modify the browser state, such as the current viewport.")
        ("r-iranges" ,r-iranges)
        ("r-rcurl" ,r-rcurl)
        ("r-rsqlite" ,r-rsqlite)
-       ("r-rmysql" ,r-rmysql)
        ("r-rtracklayer" ,r-rtracklayer)
        ("r-s4vectors" ,r-s4vectors)
        ("r-xvector" ,r-xvector)))
@@ -7734,13 +7772,13 @@ information about the latest version of the Gene Ontologies.")
 (define-public r-graph
   (package
     (name "r-graph")
-    (version "1.56.0")
+    (version "1.58.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "graph" version))
               (sha256
                (base32
-                "15aajjp8h2z14p80c8hyd4rrmr9vqsm7bvwb989jxjl4k6g52an1"))))
+                "1zx445lk36g1s6i5dbhhf00nzzazyklfjxxjfax6q8hnhvgm9759"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)))
@@ -7753,13 +7791,13 @@ information about the latest version of the Gene Ontologies.")
 (define-public r-topgo
   (package
     (name "r-topgo")
-    (version "2.30.1")
+    (version "2.32.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "topGO" version))
               (sha256
                (base32
-                "1cgz4knxr328xfqlhl6ypxl6x86rfrlqz748kn94ainxjzz55i6x"))))
+                "05yxnkid8bgw9lkm90if9fg63djhgvbailfa3qsfqa5c0zjmixw1"))))
     (properties
      `((upstream-name . "topGO")))
     (build-system r-build-system)
@@ -7786,13 +7824,13 @@ dependencies between GO terms can be implemented and applied.")
 (define-public r-bsgenome
   (package
     (name "r-bsgenome")
-    (version "1.46.0")
+    (version "1.48.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BSgenome" version))
               (sha256
                (base32
-                "1jbzq7lm2iajajn2bifxnkss0k9fdvgqr30mral17cbhp5f6w4lq"))))
+                "1rk2piqq5dppkd51ln3r872d7ng3rvq98071mnd0xdv2xwnyn5g8"))))
     (properties
      `((upstream-name . "BSgenome")))
     (build-system r-build-system)
@@ -7847,13 +7885,13 @@ genome data packages and support for efficient SNP representation.")
 (define-public r-impute
   (package
     (name "r-impute")
-    (version "1.52.0")
+    (version "1.54.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "impute" version))
               (sha256
                (base32
-                "0b8r4swvyx3cjcc2ky8yn0ncpzlbi1pgfsn3wpbjmhh7sqrffm2n"))))
+                "1d3cpfaqlq2gnb3hsc2yhxwkrnbd7m6ifif32yp0ya0jr5brl4hr"))))
     (inputs
      `(("gfortran" ,gfortran)))
     (build-system r-build-system)
@@ -7867,13 +7905,13 @@ microarray data, using nearest neighbor averaging.")
 (define-public r-seqpattern
   (package
     (name "r-seqpattern")
-    (version "1.10.0")
+    (version "1.12.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "seqPattern" version))
               (sha256
                (base32
-                "1kcm5w83q7w0v0vs7nyp4gq5z86c6n6pqy9zmyyhxcrns7f597pm"))))
+                "0dw0yldfcf0ibvpqxlpx1ijnjf9lma47w9w22siszzhw09i0wp3w"))))
     (properties
      `((upstream-name . "seqPattern")))
     (build-system r-build-system)
@@ -7894,13 +7932,13 @@ reference point and sorted by a user defined feature.")
 (define-public r-genomation
   (package
     (name "r-genomation")
-    (version "1.11.3")
+    (version "1.12.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "genomation" version))
               (sha256
                (base32
-                "1d2g1v6xhrf3gm86pv8ln22df5g6v6k6i4i39v4j82zn4apany6v"))))
+                "1vdmdyrq0n7pf8cvy2950v7hrcrcbd9zl4fg7dcmyly3iiwdyirp"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biostrings" ,r-biostrings)
@@ -8072,14 +8110,14 @@ annotations for the genome of the model mouse Mus musculus.")
 (define-public r-seqlogo
   (package
     (name "r-seqlogo")
-    (version "1.44.0")
+    (version "1.46.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "seqLogo" version))
        (sha256
         (base32
-         "1ql4q4vx0j61a893dqc3c8zxmgs8sqhy3j1qhyfdvbd01vw9w1kq"))))
+         "16xvqcdknix9vjm8mrixi6nyfsr45jm844jh1x90m8044lwrsic1"))))
     (properties `((upstream-name . "seqLogo")))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/seqLogo")
@@ -8318,14 +8356,14 @@ Biostrings objects.")
 (define-public r-motifrg
   (package
     (name "r-motifrg")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "motifRG" version))
        (sha256
         (base32
-         "193zl2rlzwxv9p9q5i7rilj3w05ndqfyp9bdpvagp5s5cin4hf44"))))
+         "0mxhyidkyd2zqahdbg69y20r550z78lvr1r3pbjymnwfg4hcfq1p"))))
     (properties `((upstream-name . "motifRG")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9085,6 +9123,19 @@ replacement for strverscmp.")
        ("python-numpy" ,python-numpy)
        ;; MultQC checks for the presence of nose at runtime.
        ("python-nose" ,python-nose)))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'relax-requirements
+           (lambda _
+             (substitute* "setup.py"
+               ;; MultiQC 1.5 ‘requires’ a version of python-matplotlib older
+               ;; than the one in Guix, but should work fine with 2.2.2.
+               ;; See <https://github.com/ewels/MultiQC/issues/725> and
+               ;; <https://github.com/ewels/MultiQC/issues/732> for details.
+               (("['\"]matplotlib.*?['\"]")
+                "'matplotlib'"))
+             #t)))))
     (home-page "http://multiqc.info")
     (synopsis "Aggregate bioinformatics analysis reports")
     (description
@@ -9638,13 +9689,13 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.")
 (define-public r-seurat
   (package
     (name "r-seurat")
-    (version "2.3.0")
+    (version "2.3.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "Seurat" version))
               (sha256
                (base32
-                "0kp3lw1s896zkjd6x2wp8qcg7wnm5b40g8vihps13f1m7j4nx7r0"))
+                "0hi59rgdrr2iqfvx5bq7yq02hbjxkjl1fzidqj14z0ypq0nzbjys"))
               ;; Delete pre-built jar.
               (snippet
                '(begin (delete-file "inst/java/ModularityOptimizer.jar")
@@ -9688,7 +9739,6 @@ Main-Class: ModularityOptimizer\n")))
        ("r-ggplot2" ,r-ggplot2)
        ("r-ggridges" ,r-ggridges)
        ("r-gplots" ,r-gplots)
-       ("r-gridextra" ,r-gridextra)
        ("r-hmisc" ,r-hmisc)
        ("r-ica" ,r-ica)
        ("r-igraph" ,r-igraph)
@@ -9709,6 +9759,7 @@ Main-Class: ModularityOptimizer\n")))
        ("r-rcppeigen" ,r-rcppeigen)
        ("r-rcppprogress" ,r-rcppprogress)
        ("r-reshape2" ,r-reshape2)
+       ("r-reticulate" ,r-reticulate)
        ("r-rocr" ,r-rocr)
        ("r-rtsne" ,r-rtsne)
        ("r-sdmtools" ,r-sdmtools)
@@ -11141,25 +11192,22 @@ with narrow binding events such as transcription factor ChIP-seq.")
 (define-public trim-galore
   (package
     (name "trim-galore")
-    (version "0.4.2")
+    (version "0.4.5")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "http://www.bioinformatics.babraham.ac.uk/"
-                           "projects/trim_galore/trim_galore_v"
-                           version ".zip"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/FelixKrueger/TrimGalore.git")
+             (commit version)))
+       (file-name (string-append name "-" version "-checkout"))
        (sha256
         (base32
-         "0b9qdxi4521gsrjvbhgky8g7kry9b5nx3byzaxkgxz7p4k8bn1mn"))))
+         "0x5892l48c816pf00wmnz5vq0zq6170d3xc8zrxncd4jcz7h1p71"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f                      ; no tests
        #:phases
        (modify-phases %standard-phases
-         ;; The archive contains plain files.
-         (replace 'unpack
-           (lambda* (#:key source #:allow-other-keys)
-             (zero? (system* "unzip" source))))
          (delete 'configure)
          (delete 'build)
          (add-after 'unpack 'hardcode-tool-references
@@ -11540,7 +11588,9 @@ browser.")
            (replace 'install
              (lambda* (#:key inputs outputs #:allow-other-keys)
                (let* ((target (assoc-ref outputs "out"))
-                      (doc (string-append target "/share/doc/f-seq/")))
+                      (bin (string-append target "/bin"))
+                      (doc (string-append target "/share/doc/f-seq"))
+                      (lib (string-append target "/lib")))
                  (mkdir-p target)
                  (mkdir-p doc)
                  (substitute* "bin/linux/fseq"
@@ -11549,11 +11599,11 @@ browser.")
                     (string-append (assoc-ref inputs "java-commons-cli")
                                    "/share/java/commons-cli.jar"))
                    (("REALDIR=.*")
-                    (string-append "REALDIR=" target "/bin\n")))
+                    (string-append "REALDIR=" bin "\n")))
                  (install-file "README.txt" doc)
-                 (install-file "bin/linux/fseq" (string-append target "/bin"))
-                 (install-file "build~/fseq.jar" (string-append target "/lib"))
-                 (copy-recursively "lib" (string-append target "/lib"))
+                 (install-file "bin/linux/fseq" bin)
+                 (install-file "build~/fseq.jar" lib)
+                 (copy-recursively "lib" lib)
                  #t))))))
       (inputs
        `(("perl" ,perl)
@@ -11571,47 +11621,61 @@ Browser.")
 (define-public bismark
   (package
     (name "bismark")
-    (version "0.16.3")
+    (version "0.19.1")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://github.com/FelixKrueger/Bismark/"
-                           "archive/" version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/FelixKrueger/Bismark.git")
+             (commit version)))
+       (file-name (string-append name "-" version "-checkout"))
        (sha256
         (base32
-         "1204i0pa02ll2jn5pnxypkclnskvv7a2nwh5nxhagmhxk9wfv9sq"))))
+         "0yb5l36slwg02fp4b1jdlplgljcsxgqfzvzihzdnphd87dghcc84"))
+       (snippet
+        '(begin
+           ;; highcharts.js is non-free software.  The code is available under
+           ;; CC-BY-NC or proprietary licenses only.
+           (delete-file "bismark_sitrep/highcharts.js")
+           #t))))
     (build-system perl-build-system)
     (arguments
-     `(#:tests? #f ; there are no tests
+     `(#:tests? #f                      ; there are no tests
        #:phases
        (modify-phases %standard-phases
          (delete 'configure)
          (delete 'build)
          (replace 'install
            (lambda* (#:key inputs outputs #:allow-other-keys)
-             (let ((bin (string-append (assoc-ref outputs "out")
-                                       "/bin"))
-                   (docdir  (string-append (assoc-ref outputs "out")
-                                           "/share/doc/bismark"))
-                   (docs    '("Bismark_User_Guide.pdf"
-                              "RELEASE_NOTES.txt"))
-                   (scripts '("bismark"
-                              "bismark_genome_preparation"
-                              "bismark_methylation_extractor"
-                              "bismark2bedGraph"
-                              "bismark2report"
-                              "coverage2cytosine"
-                              "deduplicate_bismark"
-                              "bismark_sitrep.tpl"
-                              "bam2nuc"
-                              "bismark2summary")))
+             (let* ((out (assoc-ref outputs "out"))
+                    (bin (string-append out "/bin"))
+                    (share   (string-append out "/share/bismark"))
+                    (docdir  (string-append out "/share/doc/bismark"))
+                    (docs    '("Docs/Bismark_User_Guide.html"))
+                    (scripts '("bismark"
+                               "bismark_genome_preparation"
+                               "bismark_methylation_extractor"
+                               "bismark2bedGraph"
+                               "bismark2report"
+                               "coverage2cytosine"
+                               "deduplicate_bismark"
+                               "filter_non_conversion"
+                               "bam2nuc"
+                               "bismark2summary")))
+               (substitute* "bismark2report"
+                 (("\\$RealBin/bismark_sitrep")
+                  (string-append share "/bismark_sitrep")))
+               (mkdir-p share)
                (mkdir-p docdir)
                (mkdir-p bin)
                (for-each (lambda (file) (install-file file bin))
                          scripts)
                (for-each (lambda (file) (install-file file docdir))
                          docs)
+               (copy-recursively "Docs/Images" (string-append docdir "/Images"))
+               (copy-recursively "bismark_sitrep"
+                                 (string-append share "/bismark_sitrep"))
+
                ;; Fix references to gunzip
                (substitute* (map (lambda (file)
                                    (string-append bin "/" file))
@@ -12969,7 +13033,7 @@ methylation and segmentation.")
 (define-public pigx-scrnaseq
   (package
     (name "pigx-scrnaseq")
-    (version "0.0.3")
+    (version "0.0.4")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/BIMSBbioinfo/pigx_scrnaseq/"
@@ -12977,7 +13041,7 @@ methylation and segmentation.")
                                   "/pigx_scrnaseq-" version ".tar.gz"))
               (sha256
                (base32
-                "12qdq0nj1wdkyighdxj6924bmbpd1a0b3gam6w64l4hiqrv5sijz"))))
+                "1pvjm6f3mascprs65vflggwwg5v925knvgal7k7a6nnlmw5qndrf"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags