diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 669 |
1 files changed, 400 insertions, 269 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 32b795948b..f60a918d75 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -475,20 +475,6 @@ BED, GFF/GTF, VCF.") (find-files "bin" ".*"))) #t))))))) -;; Needed for pybedtools. -(define-public bedtools-2.26 - (package (inherit bedtools) - (name "bedtools") - (version "2.26.0") - (source (origin - (method url-fetch) - (uri (string-append "https://github.com/arq5x/bedtools2/releases/" - "download/v" version "/" - "bedtools-" version ".tar.gz")) - (sha256 - (base32 - "0jhavwifnf7lmkb11h9y7dynr8d699h0rd2l52j1pfgircr2zwv5")))))) - (define-public pbbam (package (name "pbbam") @@ -806,12 +792,13 @@ intended to behave exactly the same as the original BWK awk.") ;; See https://github.com/daler/pybedtools/issues/192 #:phases (modify-phases %standard-phases - ;; See https://github.com/daler/pybedtools/issues/261 (add-after 'unpack 'disable-broken-tests (lambda _ - ;; This test (pybedtools.test.test_scripts.test_venn_mpl) needs a - ;; graphical environment. (substitute* "pybedtools/test/test_scripts.py" + ;; This test freezes. + (("def test_intron_exon_reads") + "def _do_not_test_intron_exon_reads") + ;; This test fails in the Python 2 build. (("def test_venn_mpl") "def _do_not_test_venn_mpl")) (substitute* "pybedtools/test/test_helpers.py" @@ -868,7 +855,7 @@ intended to behave exactly the same as the original BWK awk.") (mkdir-p "/tmp/test") (copy-recursively "pybedtools/test" "/tmp/test") (with-directory-excursion "/tmp/test" - (invoke "pytest"))))))) + (invoke "pytest" "-v" "--doctest-modules"))))))) (propagated-inputs `(("bedtools" ,bedtools) ("samtools" ,samtools) @@ -985,6 +972,64 @@ e.g. microbiome samples, genomes, metagenomes.") (("install_requires.append\\(\"pyqi\"\\)") "pass")) #t))))))))) +(define-public python-pairtools + (package + (name "python-pairtools") + (version "0.3.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/mirnylab/pairtools") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0gr8y13q7sd6yai6df4aavl2470n1f9s3cib6r473z4hr8hcbwmc")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-references + (lambda _ + (substitute* '("pairtools/pairtools_merge.py" + "pairtools/pairtools_sort.py") + (("/bin/bash") (which "bash"))) + #t)) + (replace 'check + (lambda* (#:key inputs outputs #:allow-other-keys) + (add-installed-pythonpath inputs outputs) + (with-directory-excursion "/tmp" + (invoke "pytest" "-v"))))))) + (native-inputs + `(("python-cython" ,python-cython) + ("python-nose" ,python-nose) + ("python-pytest" ,python-pytest))) + (inputs + `(("python" ,python-wrapper))) + (propagated-inputs + `(("htslib" ,htslib) ; for bgzip, looked up in PATH + ("samtools" ,samtools) ; looked up in PATH + ("lz4" ,lz4) ; for lz4c + ("python-click" ,python-click) + ("python-numpy" ,python-numpy))) + (home-page "https://github.com/mirnylab/pairtools") + (synopsis "Process mapped Hi-C data") + (description "Pairtools is a simple and fast command-line framework to +process sequencing data from a Hi-C experiment. Process pair-end sequence +alignments and perform the following operations: + +@itemize +@item detect ligation junctions (a.k.a. Hi-C pairs) in aligned paired-end + sequences of Hi-C DNA molecules +@item sort @code{.pairs} files for downstream analyses +@item detect, tag and remove PCR/optical duplicates +@item generate extensive statistics of Hi-C datasets +@item select Hi-C pairs given flexibly defined criteria +@item restore @code{.sam} alignments from Hi-C pairs. +@end itemize +") + (license license:expat))) + (define-public bioperl-minimal (let* ((inputs `(("perl-module-build" ,perl-module-build) ("perl-data-stag" ,perl-data-stag) @@ -1401,7 +1446,7 @@ package provides command line tools using the Bio++ library.") ("python" ,python-wrapper))) (native-inputs `(("cpio" ,cpio))) - (home-page "http://blast.ncbi.nlm.nih.gov") + (home-page "https://blast.ncbi.nlm.nih.gov") (synopsis "Basic local alignment search tool") (description "BLAST is a popular method of performing a DNA or protein sequence @@ -5723,7 +5768,7 @@ Roche 454, Ion Torrent and Pacific BioSciences SMRT.") (define-public ngs-sdk (package (name "ngs-sdk") - (version "2.9.6") + (version "2.10.5") (source (origin (method git-fetch) (uri (git-reference @@ -5732,7 +5777,7 @@ Roche 454, Ion Torrent and Pacific BioSciences SMRT.") (file-name (git-file-name name version)) (sha256 (base32 - "0d5k5kabgl15as37kj9x65xc92j4gcqms86hvihw3yb6wag0r0q3")))) + "1ix51c25hjn57w93qmwzw80xh2i34wx8j2hn7szh8p6w8i3az5qa")))) (build-system gnu-build-system) (arguments `(#:parallel-build? #f ; not supported @@ -5789,7 +5834,7 @@ simultaneously.") (define-public ncbi-vdb (package (name "ncbi-vdb") - (version "2.9.6") + (version "2.10.6") (source (origin (method git-fetch) (uri (git-reference @@ -5798,7 +5843,7 @@ simultaneously.") (file-name (git-file-name name version)) (sha256 (base32 - "0knkj1sq34hlivgv5qd6jlczqrs3ldmfgn6vbbw7p4mqxvb9mirk")))) + "0m8hlxscidsfqm9x9fyi62q6lpf1dv5115kgjjgnrkl49q9c27m6")))) (build-system gnu-build-system) (arguments `(#:parallel-build? #f ; not supported @@ -6148,7 +6193,7 @@ sequence itself can be retrieved from these databases.") (define-public sra-tools (package (name "sra-tools") - (version "2.9.6") + (version "2.10.6") (source (origin (method git-fetch) @@ -6158,11 +6203,11 @@ sequence itself can be retrieved from these databases.") (file-name (git-file-name name version)) (sha256 (base32 - "0vqzap68v81k0zif2mnqfy8pnw2nrhsg87p6mgq8qk3nk2jv2rgy")))) + "1cr2mijkfs5sm35ffjs6861qsd1qkgnhnbavdv65zg5d655abbjf")))) (build-system gnu-build-system) (arguments - `(#:parallel-build? #f ; not supported - #:tests? #f ; no "check" target + `(#:parallel-build? #f ; not supported + #:tests? #f ; no "check" target #:make-flags (list (string-append "DEFAULT_CRT=" (assoc-ref %build-inputs "ncbi-vdb") @@ -6205,6 +6250,9 @@ sequence itself can be retrieved from these databases.") ;; Dynamic linking (substitute* "tools/copycat/Makefile" (("smagic-static") "lmagic")) + (substitute* "tools/driver-tool/utf8proc/Makefile" + (("CC\\?=gcc") "myCC=gcc") + (("\\(CC\\)") "(myCC)")) ;; The 'configure' script doesn't recognize things like ;; '--enable-fast-install'. @@ -6217,8 +6265,9 @@ sequence itself can be retrieved from these databases.") (string-append "--with-magic-prefix=" (assoc-ref inputs "libmagic")) ;; TODO: building with libxml2 fails with linker errors - ;; (string-append "--with-xml2-prefix=" - ;; (assoc-ref inputs "libxml2")) + #; + (string-append "--with-xml2-prefix=" + (assoc-ref inputs "libxml2")) (string-append "--with-ncbi-vdb-sources=" (assoc-ref inputs "ncbi-vdb")) (string-append "--with-ncbi-vdb-build=" @@ -6234,8 +6283,9 @@ sequence itself can be retrieved from these databases.") ("ncbi-vdb" ,ncbi-vdb) ("libmagic" ,file) ("fuse" ,fuse) - ("hdf5" ,hdf5) - ("zlib" ,zlib))) + ("hdf5" ,hdf5-1.10) + ("zlib" ,zlib) + ("python" ,python-wrapper))) (home-page "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software") (synopsis "Tools and libraries for reading and writing sequencing data") @@ -6897,17 +6947,18 @@ information as possible.") (define-public r-genefilter (package (name "r-genefilter") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genefilter" version)) (sha256 (base32 - "1xjr02qhldspjwd6y374wgik18fgywb6408wsz471i8b4ik98ckc")))) + "1sbbrnq6p90fri0ik6aq2zw26kasw63nyiy7xkzrj6vgyq7x258g")))) (build-system r-build-system) (native-inputs - `(("gfortran" ,gfortran))) + `(("gfortran" ,gfortran) + ("r-knitr" ,r-knitr))) (propagated-inputs `(("r-annotate" ,r-annotate) ("r-annotationdbi" ,r-annotationdbi) @@ -6924,14 +6975,14 @@ high-throughput sequencing experiments.") (define-public r-deseq2 (package (name "r-deseq2") - (version "1.26.0") + (version "1.28.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq2" version)) (sha256 (base32 - "1lmbhznfs8dz9ipd53z4ccwvwxqwzx1ayw56jlrvlsambaj8fash")))) + "0xh12c2skr0bbv893p05gvbismkcnqw8zwh7yz4wmycgajfzg2pp")))) (properties `((upstream-name . "DESeq2"))) (build-system r-build-system) (propagated-inputs @@ -6942,13 +6993,14 @@ high-throughput sequencing experiments.") ("r-geneplotter" ,r-geneplotter) ("r-genomicranges" ,r-genomicranges) ("r-ggplot2" ,r-ggplot2) - ("r-hmisc" ,r-hmisc) ("r-iranges" ,r-iranges) ("r-locfit" ,r-locfit) ("r-rcpp" ,r-rcpp) ("r-rcpparmadillo" ,r-rcpparmadillo) ("r-s4vectors" ,r-s4vectors) ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/DESeq2") (synopsis "Differential gene expression analysis") (description @@ -6961,14 +7013,14 @@ distribution.") (define-public r-dexseq (package (name "r-dexseq") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DEXSeq" version)) (sha256 (base32 - "0sqqb65ckliif2nmvlvc7w49id59z0nvqcdz5gry8l2mn6azrf6a")))) + "1inyxb89hd5bn0sl7a9qbv9d1g40z4v1s9qwxkcsx5c79fl04n1h")))) (properties `((upstream-name . "DEXSeq"))) (build-system r-build-system) (propagated-inputs @@ -6989,6 +7041,8 @@ distribution.") ("r-statmod" ,r-statmod) ("r-stringr" ,r-stringr) ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/DEXSeq") (synopsis "Inference of differential exon usage in RNA-Seq") (description @@ -7004,14 +7058,14 @@ exploration of the results.") (define-public r-annotationforge (package (name "r-annotationforge") - (version "1.28.0") + (version "1.30.1") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationForge" version)) (sha256 (base32 - "0h2r60v339ajk5r6xq4iwwcpihdvf12fi8255byr2dhglzrd8xl7")))) + "1a2155jxbwc6qr3dcyvp850grhdr7czc7bs3s87ff4sgdl0jp3jw")))) (properties `((upstream-name . "AnnotationForge"))) (build-system r-build-system) @@ -7024,6 +7078,8 @@ exploration of the results.") ("r-rsqlite" ,r-rsqlite) ("r-s4vectors" ,r-s4vectors) ("r-xml" ,r-xml))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/AnnotationForge") (synopsis "Code for building annotation database packages") (description @@ -7034,14 +7090,14 @@ databases. Packages produced are intended to be used with AnnotationDbi.") (define-public r-rbgl (package (name "r-rbgl") - (version "1.62.1") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RBGL" version)) (sha256 (base32 - "0ixbkdirf08i400db587r262j52sdwdgk3884nxk5xkbhx2m6vg0")))) + "079599a6xn2i7snfn2vgshkw0c00rrfhj44pvi03ap8id29bkayy")))) (properties `((upstream-name . "RBGL"))) (build-system r-build-system) (propagated-inputs @@ -7057,14 +7113,14 @@ the graph algorithms contained in the Boost library.") (define-public r-gseabase (package (name "r-gseabase") - (version "1.48.0") + (version "1.50.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GSEABase" version)) (sha256 (base32 - "0kcb90sxlf19d5dxhdbqk9x62svky4262cccl0wxarbq6gf3bd57")))) + "1k4faj53cwvqijad8cf7fcghzxcv9shlbpl8n73bsncc8k192y2j")))) (properties `((upstream-name . "GSEABase"))) (build-system r-build-system) (propagated-inputs @@ -7074,6 +7130,8 @@ the graph algorithms contained in the Boost library.") ("r-biocgenerics" ,r-biocgenerics) ("r-graph" ,r-graph) ("r-xml" ,r-xml))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/GSEABase") (synopsis "Gene set enrichment data structures and methods") (description @@ -7084,14 +7142,14 @@ Enrichment Analysis} (GSEA).") (define-public r-category (package (name "r-category") - (version "2.52.1") + (version "2.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Category" version)) (sha256 (base32 - "0ga0ij9hyzsxa5pavwmv35i8xggia2wygrk4m4z8an0qcvgy3v5g")))) + "1grspdzk5a4vidnxwcd1jmy1vcn494aydsp3vydx235yv7iqac1b")))) (properties `((upstream-name . "Category"))) (build-system r-build-system) (propagated-inputs @@ -7115,14 +7173,14 @@ analysis.") (define-public r-gostats (package (name "r-gostats") - (version "2.52.0") + (version "2.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOstats" version)) (sha256 (base32 - "19f4gxm3sbprqrnwzvskvywv6j4ibm8xkrbgg4h0fvh2b5331nwc")))) + "00q39cyv4l28r6s9gjnd0qhl7h80vmwp4lpmchisqzj44xzyics9")))) (properties `((upstream-name . "GOstats"))) (build-system r-build-system) (propagated-inputs @@ -7146,14 +7204,14 @@ testing and other simple calculations.") (define-public r-shortread (package (name "r-shortread") - (version "1.44.3") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ShortRead" version)) (sha256 (base32 - "0ykyrj4g6vc67d5s46sp4659qvar2iavflzhggm79w4p50hxia4s")))) + "0l4kdln69y6yhln0xiv2jmpxg05fjcglln406p43a2bqvk2lr03d")))) (properties `((upstream-name . "ShortRead"))) (build-system r-build-system) (inputs @@ -7188,22 +7246,23 @@ ungapped alignment formats.") (define-public r-systempiper (package (name "r-systempiper") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "systemPipeR" version)) (sha256 (base32 - "17r25v9wcglyma2v1c8fka80dm7fx86saxlsb2aprmwi4h3dhb0j")))) + "01ilhlrvy28jfdyxjria4024yryj5zgympgqznw17g3y3az78kk2")))) (properties `((upstream-name . "systemPipeR"))) (build-system r-build-system) (propagated-inputs `(("r-annotate" ,r-annotate) + ("r-assertthat" ,r-assertthat) ("r-batchtools" ,r-batchtools) - ("r-biocgenerics" ,r-biocgenerics) ("r-biostrings" ,r-biostrings) ("r-deseq2" ,r-deseq2) + ("r-dot" ,r-dot) ("r-edger" ,r-edger) ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) @@ -7211,13 +7270,18 @@ ungapped alignment formats.") ("r-go-db" ,r-go-db) ("r-gostats" ,r-gostats) ("r-limma" ,r-limma) + ("r-magrittr" ,r-magrittr) ("r-pheatmap" ,r-pheatmap) ("r-rjson" ,r-rjson) ("r-rsamtools" ,r-rsamtools) + ("r-rsvg" ,r-rsvg) ("r-shortread" ,r-shortread) + ("r-stringr" ,r-stringr) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-yaml" ,r-yaml) ("r-variantannotation" ,r-variantannotation))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/tgirke/systemPipeR") (synopsis "Next generation sequencing workflow and reporting environment") (description @@ -7235,14 +7299,14 @@ annotation infrastructure.") (define-public r-grohmm (package (name "r-grohmm") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "groHMM" version)) (sha256 (base32 - "0ywr8f6bfhg2ia3n4rmsxr4v1xqmlyhkwh0rvkgh3yqgnbvihndg")))) + "04z9qq1xwdsaxbqhyld37w0ybvzly9pc1hcyrnwdbyjwd7n1fncb")))) (properties `((upstream-name . "groHMM"))) (build-system r-build-system) (propagated-inputs @@ -7468,13 +7532,13 @@ BLAST, KEGG, GenBank, MEDLINE and GO.") (define-public r-biocviews (package (name "r-biocviews") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biocViews" version)) (sha256 (base32 - "0yn8jys1900d31haayz0ppqk5y79mwjajwp4alz6pln3dbs70f3g")))) + "1h4cmfbff79v9xrh271dp3rv0877ris06lmkvc39kqzj7yjsh7c2")))) (properties `((upstream-name . "biocViews"))) (build-system r-build-system) @@ -7496,13 +7560,13 @@ also known as views, in a controlled vocabulary.") (define-public r-biocstyle (package (name "r-biocstyle") - (version "2.14.4") + (version "2.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocStyle" version)) (sha256 (base32 - "1x71in059zql40f4c87bd1gf96r945kdvwbq61jmch9d3d8nwxbb")))) + "07rjl2n4sazdg581zh7w3yykzphgr2gpz41ba4ryqs7347vh9nbf")))) (properties `((upstream-name . "BiocStyle"))) (build-system r-build-system) @@ -7512,6 +7576,8 @@ also known as views, in a controlled vocabulary.") ("r-knitr" ,r-knitr) ("r-rmarkdown" ,r-rmarkdown) ("r-yaml" ,r-yaml))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/BiocStyle") (synopsis "Bioconductor formatting styles") (description "This package provides standard formatting styles for @@ -7522,13 +7588,13 @@ functionality.") (define-public r-bioccheck (package (name "r-bioccheck") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocCheck" version)) (sha256 (base32 - "1qnvl5yajgh67ijkq6gdsafri1k5hyw5gzn2ccqk9ymx6i2xd80g")))) + "1p9ys18sn1crxw1iac2jdgqvwpb5hjd9nfxx0qn0ncrv0b550mny")))) (properties `((upstream-name . "BiocCheck"))) (build-system r-build-system) @@ -7560,6 +7626,8 @@ functionality.") ("r-biocmanager" ,r-biocmanager) ("r-biocviews" ,r-biocviews) ("r-stringdist" ,r-stringdist))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/BiocCheck") (synopsis "Executes Bioconductor-specific package checks") (description "This package contains tools to perform additional quality @@ -7569,13 +7637,13 @@ checks on R packages that are to be submitted to the Bioconductor repository.") (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.24.4") + (version "0.26.1") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "1fzs8j2d3wwfzm2fq63ywf68a4dbggyl5l098f148yn4jw7jd3bc")))) + "1ddr3ngyczx332zw9ai1a6h7442lgrbfcj8vrhvbkdkzqwj14xmb")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) @@ -7596,13 +7664,13 @@ S4Vectors package itself.") (define-public r-iranges (package (name "r-iranges") - (version "2.20.2") + (version "2.22.2") (source (origin (method url-fetch) (uri (bioconductor-uri "IRanges" version)) (sha256 (base32 - "1jhnxb9yacmj2z82b6992gihjvj1a0gnjwbjiagyyx03fqnv23kg")))) + "1y24jw62806wp2afiyj1x6n00gj7d3323klqdypra9q43pg1w49d")))) (properties `((upstream-name . "IRanges"))) (build-system r-build-system) @@ -7648,13 +7716,13 @@ ID and species. It is used by functions in the GenomeInfoDb package.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.22.1") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "0phadr67yb4l25x41a9wg4pjy1wbxlk14jhidhz6g5n4z6x45qbm")))) + "0ab92nq7lvhvhgp512qhiiphpby0b17c666qska6p8a636zzmqiv")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) @@ -7678,13 +7746,13 @@ names in their natural, rather than lexicographic, order.") (define-public r-edger (package (name "r-edger") - (version "3.28.1") + (version "3.30.3") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "07dv99kl7jfa62nzcq705r56gcpb1hq7p4px48j71y2ddi1rqmr6")))) + "1z9bkg08rgqn3jm2s4ndbj641w33wl8jd3j6m5if6h2nnw6011ic")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs @@ -7706,13 +7774,13 @@ CAGE.") (define-public r-variantannotation (package (name "r-variantannotation") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantAnnotation" version)) (sha256 (base32 - "009s7rzp78s2w6iybizina42qx2w8qv3xwjbkpqphmm451maykgs")))) + "09y6ymwky839nb0y7y93w810hk9mvwqn7595q1276c28dkddiqvw")))) (properties `((upstream-name . "VariantAnnotation"))) (inputs @@ -7745,13 +7813,13 @@ coding changes and predict coding outcomes.") (define-public r-limma (package (name "r-limma") - (version "3.42.2") + (version "3.44.1") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "1nd01r7rd7jb5qz84vbgfnyrmgm9wiq7fsdji68537kjgvrzmm9z")))) + "0l6f6lz1rghj8c5s14ljbnmsrwz27fi6a7g42n15n3d3msvflw36")))) (build-system r-build-system) (home-page "http://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") @@ -7764,13 +7832,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") (define-public r-xvector (package (name "r-xvector") - (version "0.26.0") + (version "0.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "XVector" version)) (sha256 (base32 - "0s2gg84yzl5ffkzp6n7kh0jjk1vd90z189f5hkfn18rn67cy2nv7")))) + "11h1hszv4798q1gbx8r6zf8vlaqx4v9ql0lbh2xaxybp66a03pvc")))) (properties `((upstream-name . "XVector"))) (build-system r-build-system) @@ -7800,13 +7868,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") (define-public r-genomicranges (package (name "r-genomicranges") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicRanges" version)) (sha256 (base32 - "0xdds6ws7jjdfy4x3mb0qhy43kpxdmifmpw0jdk4wgw999zabb50")))) + "0wn1zr2qq0rpv9z2wialgizn6xzdlcjg1w2kif67n53svz6vk2x1")))) (properties `((upstream-name . "GenomicRanges"))) (build-system r-build-system) @@ -7816,6 +7884,8 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") ("r-iranges" ,r-iranges) ("r-s4vectors" ,r-s4vectors) ("r-xvector" ,r-xvector))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/GenomicRanges") (synopsis "Representation and manipulation of genomic intervals") (description @@ -7829,13 +7899,13 @@ manipulating genomic intervals and variables defined along a genome.") (define-public r-biobase (package (name "r-biobase") - (version "2.46.0") + (version "2.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biobase" version)) (sha256 (base32 - "1gx41083dqlm59vwqdxvc4ny31x91j48mda9n3scg0f2zwasvqgl")))) + "13p3kgnxm7hbn8cy289kbhaiyfa6rxx7l1pbvajwqzbay3cxznqp")))) (properties `((upstream-name . "Biobase"))) (build-system r-build-system) @@ -7851,13 +7921,13 @@ on Bioconductor or which replace R functions.") (define-public r-annotationdbi (package (name "r-annotationdbi") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationDbi" version)) (sha256 (base32 - "09piz1f0xpbb4amskx4ilby6lfrn27hhwk75il2c4lq6m3hr4w8s")))) + "10gplxal0qphcn29azv0i6hiim9q45lmhzvhhhsnwfhwpgja7p05")))) (properties `((upstream-name . "AnnotationDbi"))) (build-system r-build-system) @@ -7868,6 +7938,8 @@ on Bioconductor or which replace R functions.") ("r-iranges" ,r-iranges) ("r-rsqlite" ,r-rsqlite) ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/AnnotationDbi") (synopsis "Annotation database interface") (description @@ -7878,13 +7950,13 @@ annotation data packages using SQLite data storage.") (define-public r-biomart (package (name "r-biomart") - (version "2.42.1") + (version "2.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "0676s8aq9xj2pdrfk28kf5j69fmssn900k4vxrp11ghwjr8z24h7")))) + "0ag26q9283p9mfz4zx8qnx1w7b7ilmsb8wyx737z9cqy9a0i57wj")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) @@ -7915,13 +7987,13 @@ powerful online queries from gene annotation to database mining.") (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.20.1") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "0g0znb4whsvb9hpwx9xaasdi5n4vjqw8cpdyqgrdrjm91rls1h21")))) + "1lsg5xm5j3ly5k60fidzhkgqc9jgscyfkqngjvd9qp6yfzvsb82g")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) @@ -7929,6 +8001,8 @@ powerful online queries from gene annotation to database mining.") `(("r-futile-logger" ,r-futile-logger) ("r-snow" ,r-snow) ("r-bh" ,r-bh))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/BiocParallel") (synopsis "Bioconductor facilities for parallel evaluation") (description @@ -7940,18 +8014,19 @@ objects.") (define-public r-biostrings (package (name "r-biostrings") - (version "2.54.0") + (version "2.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biostrings" version)) (sha256 (base32 - "0pq7g2hflx2cjlpwdj6mscw9hnxvlf5y50dxf48lbrf9r3q9kmyp")))) + "0imhfz7dg8b3l5qzipjranqqshdsg2x6zc49drlhn8sc7j40cvi8")))) (properties `((upstream-name . "Biostrings"))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) + ("r-crayon" ,r-crayon) ("r-iranges" ,r-iranges) ("r-s4vectors" ,r-s4vectors) ("r-xvector" ,r-xvector))) @@ -7966,13 +8041,13 @@ biological sequences or sets of sequences.") (define-public r-rsamtools (package (name "r-rsamtools") - (version "2.2.3") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsamtools" version)) (sha256 (base32 - "1vj43acawqqkf9yval9fzxarpsf04fmn78m2hq4f083w1k0myhyr")))) + "0z01z0s71f941k7sns46nyabps28c69d6jxx6sppjpc6h4vrw0vq")))) (properties `((upstream-name . "Rsamtools"))) (build-system r-build-system) @@ -8011,19 +8086,18 @@ tab-delimited (tabix) files.") (define-public r-delayedarray (package (name "r-delayedarray") - (version "0.12.3") + (version "0.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedArray" version)) (sha256 (base32 - "02i88ll2d7r83nk0wdj28akvsz3jq19g6ixpaahfy3jy5av4byv6")))) + "1lz7a0rrlfv3w44n073mk8pw39z7lfs0njdxp5vpp0rdsmvdf1qk")))) (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-matrix" ,r-matrix) @@ -8045,13 +8119,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns), (define-public r-summarizedexperiment (package (name "r-summarizedexperiment") - (version "1.16.1") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "SummarizedExperiment" version)) (sha256 (base32 - "1z9bdk49dajafkfvv99nv6zyn6v70iyyy2jgdp5w5z8174a2bnn1")))) + "07rc79k5dp0dnf4dvsxif995aa9cgfkf13yf84qnwl64k9pf3c2c")))) (properties `((upstream-name . "SummarizedExperiment"))) (build-system r-build-system) @@ -8064,6 +8138,8 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns), ("r-iranges" ,r-iranges) ("r-matrix" ,r-matrix) ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/SummarizedExperiment") (synopsis "Container for representing genomic ranges by sample") (description @@ -8076,13 +8152,13 @@ samples.") (define-public r-genomicalignments (package (name "r-genomicalignments") - (version "1.22.1") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicAlignments" version)) (sha256 (base32 - "065xvy4pkda0ajvl1b75iski95k1pnbhxwdq7vkfl8v55915vqh6")))) + "0v8k6d7frm5p48cmk4zik78cw9abz4inx0zhl4zrmmx31ifyvk8d")))) (properties `((upstream-name . "GenomicAlignments"))) (build-system r-build-system) @@ -8109,13 +8185,13 @@ alignments.") (define-public r-rtracklayer (package (name "r-rtracklayer") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rtracklayer" version)) (sha256 (base32 - "0lp9xsm8kqrgpwgwj7qaqcv1z6qynbz084grlpwp94zsp2ppf0n6")))) + "1zcgk92sidhy4y7ws9ms4nkkh2hnccfhfh53qgna0kma9jy4v5xf")))) (build-system r-build-system) (arguments `(#:phases @@ -8156,13 +8232,13 @@ as well as query and modify the browser state, such as the current viewport.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.38.2") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "0dd226kgks50jdx5w35f3wmg95hy8aibi4kcn8p5kmqp5i8j580b")))) + "09ffsflk2yhhj9ivm028y3qdkvv8idgxpm4il3y9rym7shc8b3f8")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) @@ -8181,6 +8257,8 @@ as well as query and modify the browser state, such as the current viewport.") ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors) ("r-xvector" ,r-xvector))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/GenomicFeatures") (synopsis "Tools for working with transcript centric annotations") (description @@ -8221,13 +8299,13 @@ information about the latest version of the Gene Ontologies.") (define-public r-topgo (package (name "r-topgo") - (version "2.38.1") + (version "2.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "topGO" version)) (sha256 (base32 - "1kw9m2j67895k58lx9msc248pjwblp8clxwgsl01cql7sgi1xzlf")))) + "13rhbvn27sj75fklf1cnjaazacx8yyjlhqlnbp5zk157q6y5cwdr")))) (properties `((upstream-name . "topGO"))) (build-system r-build-system) @@ -8254,13 +8332,13 @@ dependencies between GO terms can be implemented and applied.") (define-public r-bsgenome (package (name "r-bsgenome") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BSgenome" version)) (sha256 (base32 - "0nn1b3h4hmnx5whf2cmzmyxdrcf4myj8c38rwr0sw4rc07xfzndy")))) + "1jw8r1qm9fpg2s1cw2y4np243jjxm65j2xdy2785h8fc1b02msf6")))) (properties `((upstream-name . "BSgenome"))) (build-system r-build-system) @@ -8270,6 +8348,7 @@ dependencies between GO terms can be implemented and applied.") ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) + ("r-matrixstats" ,r-matrixstats) ("r-rsamtools" ,r-rsamtools) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors) @@ -8284,13 +8363,13 @@ genome data packages and support for efficient SNP representation.") (define-public r-impute (package (name "r-impute") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "impute" version)) (sha256 (base32 - "0igz1phjd1j9bg9z4kyy7j8v9bxi9sdwz4df26r51i2vavlbrf4q")))) + "161p6l1cp3wwdynkxwvg0yhrh6yv20brdlplw5w5mavn4hf1nm0h")))) (native-inputs `(("gfortran" ,gfortran))) (build-system r-build-system) @@ -8304,13 +8383,13 @@ microarray data, using nearest neighbor averaging.") (define-public r-seqpattern (package (name "r-seqpattern") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqPattern" version)) (sha256 (base32 - "1gxrq6s2hiyac69idh5r1nbr1s69n0hg4ap2skm4g6857av9pwqf")))) + "0f1yvx2ri1557rzjx08q5bgml1cvkm8hjl8xn1qi4rjs64sy6mci")))) (properties `((upstream-name . "seqPattern"))) (build-system r-build-system) @@ -8331,13 +8410,13 @@ reference point and sorted by a user defined feature.") (define-public r-genomation (package (name "r-genomation") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genomation" version)) (sha256 (base32 - "1sba928h23b67gr3i4yj1bg655g24l3bcgsf5gvymzrv5idrss1l")))) + "1cy8kqwddiha5jy6nda1al956i4wncbgjkrxwijdb08cmka2sfwh")))) (build-system r-build-system) (propagated-inputs `(("r-biostrings" ,r-biostrings) @@ -8361,6 +8440,8 @@ reference point and sorted by a user defined feature.") ("r-runit" ,r-runit) ("r-s4vectors" ,r-s4vectors) ("r-seqpattern" ,r-seqpattern))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "http://bioinformatics.mdc-berlin.de/genomation/") (synopsis "Summary, annotation and visualization of genomic data") (description @@ -8405,14 +8486,14 @@ downloaded from Encode.") (define-public r-seqlogo (package (name "r-seqlogo") - (version "1.52.0") + (version "1.54.3") (source (origin (method url-fetch) (uri (bioconductor-uri "seqLogo" version)) (sha256 (base32 - "0s94aahp8ma1crmp83dz65ifjwrx6wqi3q6005lmbp8yk2x1rkj4")))) + "09kkxir305fv8z2yyihvspkrzclxbw1cx5mvhfkrhl10rap6662j")))) (properties `((upstream-name . "seqLogo"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/seqLogo") @@ -8426,14 +8507,14 @@ Stephens (1990).") (define-public r-motifrg (package (name "r-motifrg") - (version "1.30.0") + (version "1.31.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifRG" version)) (sha256 (base32 - "0s6wdr036lra9x93r9k8wvicbkgzypjh3jp46h92yacw8d829k0d")))) + "1ml6zyzlk8yjbnfhga2qnw8nl43rankvka0kc1yljxr2b66aqbhn")))) (properties `((upstream-name . "motifRG"))) (build-system r-build-system) (propagated-inputs @@ -8507,13 +8588,13 @@ R/qtl, to better handle high-dimensional data and complex cross designs.") (define-public r-zlibbioc (package (name "r-zlibbioc") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zlibbioc" version)) (sha256 (base32 - "1xh7qan0w62mzsmanbx9vcj6ygdfhzw1abaxijkq7f4nh5w87idj")))) + "0j1l052jb2cwc1nifxzwknc9csagf4f2d092zs0i95dz0rma89l0")))) (properties `((upstream-name . "zlibbioc"))) (build-system r-build-system) @@ -8549,14 +8630,14 @@ secondary structure and comparative analysis in R.") (define-public r-rhtslib (package (name "r-rhtslib") - (version "1.18.1") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhtslib" version)) (sha256 (base32 - "0gkbrmrcg55c9s5166ifljlx0v25rv4ijdyp4wf4c292xd6chy2l")))) + "186r7icrkzrni1c4n33ip7dlsfgys7hnqf0simvxrpl3yhh3ygdi")))) (properties `((upstream-name . "Rhtslib"))) (build-system r-build-system) ;; Without this a temporary directory ends up in the Rhtslib.so binary, @@ -8568,7 +8649,8 @@ secondary structure and comparative analysis in R.") (inputs `(("zlib" ,zlib))) (native-inputs - `(("pkg-config" ,pkg-config))) + `(("pkg-config" ,pkg-config) + ("r-knitr" ,r-knitr))) (home-page "https://github.com/nhayden/Rhtslib") (synopsis "High-throughput sequencing library as an R package") (description @@ -8580,14 +8662,14 @@ of other R packages who wish to make use of HTSlib.") (define-public r-bamsignals (package (name "r-bamsignals") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bamsignals" version)) (sha256 (base32 - "0699b0pqbs0dvs91yjibcjc90lxj9mg8rcml4a6wchfr9md7n74w")))) + "0p858xxfv79yc8b3lq58zl9f00irvbn3czsd8wdi5040xg42m402")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -8598,6 +8680,8 @@ of other R packages who wish to make use of HTSlib.") ("r-zlibbioc" ,r-zlibbioc))) (inputs `(("zlib" ,zlib))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/bamsignals") (synopsis "Extract read count signals from bam files") (description @@ -8610,24 +8694,22 @@ paired-end data.") (define-public r-rcas (package (name "r-rcas") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RCAS" version)) (sha256 (base32 - "1s3gvvxi1029d1vfwnjh21nnw3mlx08kcwz63891hml9y850cvsn")))) + "0f812pgv3ys1zv4n9sqkgm01hj4cdd0i0h85dqbhkwd94zl6cavl")))) (properties `((upstream-name . "RCAS"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biomart" ,r-biomart) + `(("r-biocgenerics" ,r-biocgenerics) ("r-biostrings" ,r-biostrings) + ("r-bsgenome" ,r-bsgenome) ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) ("r-cowplot" ,r-cowplot) ("r-data-table" ,r-data-table) - ("r-dbi" ,r-dbi) ("r-dt" ,r-dt) ("r-genomation" ,r-genomation) ("r-genomeinfodb" ,r-genomeinfodb) @@ -8635,20 +8717,21 @@ paired-end data.") ("r-genomicranges" ,r-genomicranges) ("r-ggplot2" ,r-ggplot2) ("r-ggseqlogo" ,r-ggseqlogo) - ("r-knitr" ,r-knitr) - ("r-motifrg" ,r-motifrg) - ("r-org-hs-eg-db" ,r-org-hs-eg-db) + ("r-gprofiler2" ,r-gprofiler2) + ("r-iranges" ,r-iranges) ("r-pbapply" ,r-pbapply) ("r-pheatmap" ,r-pheatmap) ("r-plotly" ,r-plotly) ("r-plotrix" ,r-plotrix) ("r-proxy" ,r-proxy) + ("r-ranger" ,r-ranger) ("r-rsqlite" ,r-rsqlite) ("r-rtracklayer" ,r-rtracklayer) ("r-rmarkdown" ,r-rmarkdown) ("r-s4vectors" ,r-s4vectors) - ("r-topgo" ,r-topgo) ("pandoc" ,ghc-pandoc))) + (native-inputs + `(("r-knitr" ,r-knitr))) (synopsis "RNA-centric annotation system") (description "RCAS aims to be a standalone RNA-centric annotation system that provides @@ -8697,9 +8780,9 @@ library implementing most of the pipeline's features.") (inputs `(("r-minimal" ,r-minimal) ("r-rcas" ,r-rcas) - ("guile-next" ,guile-2.2) + ("guile" ,guile-2.2) ("guile-json" ,guile-json-1) - ("guile-redis" ,guile-redis))) + ("guile-redis" ,guile2.2-redis))) (native-inputs `(("pkg-config" ,pkg-config))) (home-page "https://github.com/BIMSBbioinfo/rcas-web") @@ -8711,14 +8794,14 @@ library implementing most of the pipeline's features.") (define-public r-mutationalpatterns (package (name "r-mutationalpatterns") - (version "1.12.0") + (version "2.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MutationalPatterns" version)) (sha256 (base32 - "08715l6swrlccviw7932v5hyrd2x4c6049vy9qnxk0lw3sp1zvsf")))) + "02lyjiabyhmifycksvpcx29a0pb7z9xjw0hgg8n0sd0dy3afqhcm")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -8816,13 +8899,13 @@ factors bound at the specific regions.") (define-public r-tximport (package (name "r-tximport") - (version "1.14.2") + (version "1.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "tximport" version)) (sha256 (base32 - "1avy0zhgnszmg0dr9w74yq9ml10kwdrrgcni2wysrd48zzskc1n0")))) + "1x9959lkjl2h869rgd1b30q1idxzjkr1fyqbpndqk3kbi4q2gr40")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) @@ -8840,18 +8923,20 @@ of gene-level counts.") (define-public r-rhdf5 (package (name "r-rhdf5") - (version "2.30.1") + (version "2.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5" version)) (sha256 (base32 - "18pv74jj4wr1981r92ss10qkgf5g1b09dsbz3im3j70a4l5l0df0")))) + "097znwl95y2vd6asyqxs62m7binwxqmna7ss0302yl3b0s72skcy")))) (build-system r-build-system) (propagated-inputs `(("r-rhdf5lib" ,r-rhdf5lib))) (inputs `(("zlib" ,zlib))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/rhdf5") (synopsis "HDF5 interface to R") (description @@ -8867,19 +8952,21 @@ the available RAM.") (define-public r-annotationfilter (package (name "r-annotationfilter") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationFilter" version)) (sha256 (base32 - "1l9sxhlvnwn6327vgg02h11ppmqr2zr07ff8wmcng0i1jbqwa8q5")))) + "18kh1xrhpwb48s1qj4f1v8af3jmw49pnbp5afi2myn9894hxg0cs")))) (properties `((upstream-name . "AnnotationFilter"))) (build-system r-build-system) (propagated-inputs `(("r-genomicranges" ,r-genomicranges) ("r-lazyeval" ,r-lazyeval))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/Bioconductor/AnnotationFilter") (synopsis "Facilities for filtering Bioconductor annotation resources") (description @@ -9212,14 +9299,14 @@ manipulate and analyze genetic variants.") (define-public r-chipseq (package (name "r-chipseq") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chipseq" version)) (sha256 (base32 - "1ln6bn08xig3j6ryak1xfkjhvpnlm2vf1czz9hlj6f02299nbs6l")))) + "0lh859s0aq73vac1phcgagf6n000qgq2xsk0bmfr61n5swifml2a")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -9264,14 +9351,14 @@ GenomicRanges Bioconductor package.") (define-public r-copywriter (package (name "r-copywriter") - (version "2.18.0") + (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CopywriteR" version)) (sha256 (base32 - "0llg1zpxg7qnvja5f5w1z1xic0jdg6zc4mfn97h2sm44skxxcyl1")))) + "0c36wpv0rygkbqpf3dwh5xmc3lr7p8lrdzsq2fbbpw04skl6i7m2")))) (properties `((upstream-name . "CopywriteR"))) (build-system r-build-system) (propagated-inputs @@ -9304,13 +9391,13 @@ number detection tools.") (define-public r-methylkit (package (name "r-methylkit") - (version "1.12.0") + (version "1.14.2") (source (origin (method url-fetch) (uri (bioconductor-uri "methylKit" version)) (sha256 (base32 - "0klwc0sbmrxj1lxbz16pl39rxjm0pi57gjw547hlgnac1p9fspzy")))) + "1qr13d2712ypbn96ijic2z5adr5dsd61kzscx7shw6vyj360rlm5")))) (properties `((upstream-name . "methylKit"))) (build-system r-build-system) (propagated-inputs @@ -9353,17 +9440,18 @@ TAB-Seq.") (define-public r-sva (package (name "r-sva") - (version "3.34.0") + (version "3.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sva" version)) (sha256 (base32 - "1bzms6idx30s4nxl610zwa8rjxsyxb5pf3vxsdfmxg8j4pab9gh1")))) + "0xa1lm0k1a6nig90mab6xh4gln88rbs5l1cdr6ik6agg7jhs7ji4")))) (build-system r-build-system) (propagated-inputs - `(("r-genefilter" ,r-genefilter) + `(("r-edger" ,r-edger) + ("r-genefilter" ,r-genefilter) ("r-mgcv" ,r-mgcv) ("r-biocparallel" ,r-biocparallel) ("r-matrixstats" ,r-matrixstats) @@ -9463,14 +9551,14 @@ as allowing spectra with different resolutions.") (define-public r-protgenerics (package (name "r-protgenerics") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ProtGenerics" version)) (sha256 (base32 - "1k1ggjgx2la8b21841a4ngkp6xfxwz0czv7x960r7i1jqif8y48z")))) + "14xzdh7vxss8vmrw91hcwrszdn3ikm71mah8875b2lkrkrfzbl73")))) (properties `((upstream-name . "ProtGenerics"))) (build-system r-build-system) (home-page "https://github.com/lgatto/ProtGenerics") @@ -9483,14 +9571,14 @@ proteomics packages.") (define-public r-mzr (package (name "r-mzr") - (version "2.20.0") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzR" version)) (sha256 (base32 - "1cwd7phlc5jbx6r6cznyfbdpvcin5fvsaasbbi65zn0s92a80r13")) + "1r8j8yiz5lcan7j4h37sza2kwczl48dxvld3da3ghjjq67cdc2cm")) (modules '((guix build utils))) (snippet '(begin @@ -9512,7 +9600,7 @@ proteomics packages.") #t))))) (inputs `(;; Our default boost package won't work here, unfortunately, even with - ;; mzR version 2.20.0. + ;; mzR version 2.22.0. ("boost" ,boost-for-mysql) ; use this instead of the bundled boost sources ("zlib" ,zlib))) (propagated-inputs @@ -9523,6 +9611,8 @@ proteomics packages.") ("r-rcpp" ,r-rcpp) ("r-rhdf5lib" ,r-rhdf5lib) ("r-zlibbioc" ,r-zlibbioc))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/sneumann/mzR/") (synopsis "Parser for mass spectrometry data files") (description @@ -9537,14 +9627,14 @@ previously been used in XCMS.") (define-public r-affyio (package (name "r-affyio") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyio" version)) (sha256 (base32 - "0sbkadxdlx7qzxc8z8iv90y6j9b2f62mk3i54dijjh56x3hjy3hb")))) + "0j1f61409yq6hmkqrpzamfm7dx35rlq33ccs7wb1qcqx3d3nb75q")))) (build-system r-build-system) (propagated-inputs `(("r-zlibbioc" ,r-zlibbioc))) @@ -9561,14 +9651,14 @@ CDF file formats.") (define-public r-affy (package (name "r-affy") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affy" version)) (sha256 (base32 - "131za66wbaz9y86gvjqcc2yd1f2ngl2b796xw726g75djhdgxgap")))) + "0m6hkyjxmsf80n3anhwh9k26csxczv6v92fkb7klnchdski61pyc")))) (build-system r-build-system) (propagated-inputs `(("r-affyio" ,r-affyio) @@ -9589,14 +9679,14 @@ analysis.") (define-public r-vsn (package (name "r-vsn") - (version "3.54.0") + (version "3.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "vsn" version)) (sha256 (base32 - "1naqzb2m0km8fzr6chf9z71sisrwviy1fdi9b3hn4i8p18b4kqzh")))) + "1k82dikrv1gcync5y1131wg7z1kxv2z2jl4nndg20bixc3398h58")))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) @@ -9625,14 +9715,14 @@ and specific in detecting differential transcription.") (define-public r-mzid (package (name "r-mzid") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzID" version)) (sha256 (base32 - "1glcv096bn6pxlw89dlij1nzpwnjvrbxysvw2gm6qgm7rhxlaxrw")))) + "0y50lzkdamkpz67f6r5whp246qsxpbammjil7g8vjprx0c4jk5n5")))) (properties `((upstream-name . "mzID"))) (build-system r-build-system) (propagated-inputs @@ -9643,6 +9733,8 @@ and specific in detecting differential transcription.") ("r-protgenerics" ,r-protgenerics) ("r-rcpp" ,r-rcpp) ("r-xml" ,r-xml))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/mzID") (synopsis "Parser for mzIdentML files") (description @@ -9655,14 +9747,14 @@ specific parser.") (define-public r-pcamethods (package (name "r-pcamethods") - (version "1.78.0") + (version "1.80.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pcaMethods" version)) (sha256 (base32 - "1wir67kfjm0m9gf0ki8qmvh45n4gx2k0wfl9pd1hp4g62fbrj1pj")))) + "10cww4jxyynkwxbbsx804nwac31j0hh8dgisygld0q663gaxkgni")))) (properties `((upstream-name . "pcaMethods"))) (build-system r-build-system) (propagated-inputs @@ -9685,14 +9777,14 @@ structure (pcaRes) to provide a common interface to the PCA results.") (define-public r-msnbase (package (name "r-msnbase") - (version "2.12.0") + (version "2.14.2") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnbase" version)) (sha256 (base32 - "1z889xkfphqqmv31i8hh5xqyclv660ic26rfck5bjpgk3s2zzwi6")))) + "17vlv9gh41s1hp043b7j1jfqiw52alh1misjzy1kxl0g90rld00l")))) (properties `((upstream-name . "MSnbase"))) (build-system r-build-system) (propagated-inputs @@ -9718,6 +9810,8 @@ structure (pcaRes) to provide a common interface to the PCA results.") ("r-scales" ,r-scales) ("r-vsn" ,r-vsn) ("r-xml" ,r-xml))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/lgatto/MSnbase") (synopsis "Base functions and classes for MS-based proteomics") (description @@ -9728,14 +9822,14 @@ of mass spectrometry based proteomics data.") (define-public r-msnid (package (name "r-msnid") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnID" version)) (sha256 (base32 - "0m71f2y12hmwvng45kzz4r4qrgc2jbd7j9gprmw8y5laawpdaifg")))) + "0dwa6j2nqb3223a8g4f453aznjh69wngrpvdi12iy69j1psbbjcc")))) (properties `((upstream-name . "MSnID"))) (build-system r-build-system) (propagated-inputs @@ -9828,14 +9922,14 @@ discovery of differentially expressed genes and markers.") (define-public r-aroma-light (package (name "r-aroma-light") - (version "3.16.0") + (version "3.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "aroma.light" version)) (sha256 (base32 - "0cgdg650j4dl0b45pwaw49ib97dwjazrv9sqzkygrjmcnnfxry8x")))) + "19y5f2minx2pp73zdh43v1qkwpkaxygkl8cwlnwja15i46s0bcyc")))) (properties `((upstream-name . "aroma.light"))) (build-system r-build-system) (propagated-inputs @@ -9855,14 +9949,14 @@ classes.") (define-public r-deseq (package (name "r-deseq") - (version "1.38.0") + (version "1.39.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq" version)) (sha256 (base32 - "14pys93gsl50xmq5pc7pp1g20v3ywlg0yzkkhwb3kiy8573xn9nc")))) + "047hph5aqmjnz1aqprziw0smdn5lf96hmwpnvqrxv1j2yfvcf3h1")))) (properties `((upstream-name . "DESeq"))) (build-system r-build-system) (propagated-inputs @@ -9886,14 +9980,14 @@ distribution.") (define-public r-edaseq (package (name "r-edaseq") - (version "2.20.0") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EDASeq" version)) (sha256 (base32 - "19mgzbv8yxgvw86wpq401l27q55ygawlngl775yavwccz1zbhjnj")))) + "12gzxjh73qshlwvsf92lbrf4bi199kxg2snrkprh1z4yqf7bjfm4")))) (properties `((upstream-name . "EDASeq"))) (build-system r-build-system) (propagated-inputs @@ -9910,6 +10004,8 @@ distribution.") ("r-iranges" ,r-iranges) ("r-rsamtools" ,r-rsamtools) ("r-shortread" ,r-shortread))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/drisso/EDASeq") (synopsis "Exploratory data analysis and normalization for RNA-Seq") (description @@ -9925,20 +10021,23 @@ global-scaling and full-quantile normalization.") (define-public r-interactivedisplaybase (package (name "r-interactivedisplaybase") - (version "1.24.0") + (version "1.26.3") (source (origin (method url-fetch) (uri (bioconductor-uri "interactiveDisplayBase" version)) (sha256 (base32 - "0zwf3ma6wf4zypl6bgjp0n72k2hmp0g16gzl4v3y4157rxcbpl0n")))) + "1x5vipqa4pgwpd62c1c58shnlpv3zyzzpf4wdwr00q1swkdb7wv3")))) (properties `((upstream-name . "interactiveDisplayBase"))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) + ("r-dt" ,r-dt) ("r-shiny" ,r-shiny))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/interactiveDisplayBase") (synopsis "Base package for web displays of Bioconductor objects") (description @@ -9949,14 +10048,14 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-annotationhub (package (name "r-annotationhub") - (version "2.18.0") + (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationHub" version)) (sha256 (base32 - "19vj3bk8jz68q84g3j8xs1s9bqz90lbwbciig1h45zvn2zc6087m")))) + "0r4xzf93bm9cpys5cg70wg0b8hxli80hvqwgh4hzbd45yyf5c4wz")))) (properties `((upstream-name . "AnnotationHub"))) (build-system r-build-system) (propagated-inputs @@ -9973,6 +10072,8 @@ Shiny-based display methods for Bioconductor objects.") ("r-rsqlite" ,r-rsqlite) ("r-s4vectors" ,r-s4vectors) ("r-yaml" ,r-yaml))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/AnnotationHub") (synopsis "Client to access AnnotationHub resources") (description @@ -9988,14 +10089,14 @@ by the user, helping with quick and reproducible access.") (define-public r-fastseg (package (name "r-fastseg") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fastseg" version)) (sha256 (base32 - "1cys6frmbizc8bf933mwvvnr31sfya9ahcc0wm66pbd1x3mygkmk")))) + "1d48n245pzmvcpsz93lxb4frqh222gfhpmlvm0sb74skn16way63")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -10018,20 +10119,22 @@ microarrays or GRanges for sequencing data.") (define-public r-keggrest (package (name "r-keggrest") - (version "1.26.1") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGREST" version)) (sha256 (base32 - "1cgjvv9n88y3ah21356mh8z2l08vjn42hjy8hcljsibknzc4v247")))) + "0q76w17fya2x0z7mvyhkk5kqh07flldgih13ma44vhcy1bdlm6j1")))) (properties `((upstream-name . "KEGGREST"))) (build-system r-build-system) (propagated-inputs `(("r-biostrings" ,r-biostrings) ("r-httr" ,r-httr) ("r-png" ,r-png))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/KEGGREST") (synopsis "Client-side REST access to KEGG") (description @@ -10042,14 +10145,14 @@ microarrays or GRanges for sequencing data.") (define-public r-gage (package (name "r-gage") - (version "2.36.0") + (version "2.37.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gage" version)) (sha256 (base32 - "1qxfmg0id19iy3ia8h5nrvk3d1azqb28kl7m08i23654wb6b45c6")))) + "1zfaas4x6g7wiml6cmxa7b4f43az9s0lrw80k6sf7c96hsh1jijr")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -10072,14 +10175,14 @@ analysis using other methods.") (define-public r-genomicfiles (package (name "r-genomicfiles") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFiles" version)) (sha256 (base32 - "1x6q827ms2l5lwzha1vsgfrshh35n9f19jq57xagrqlafxgpz86s")))) + "1k3824pzf9fdqvcv6cz2742q3mabpmncrc72hwa21ac8wy1b04n4")))) (properties `((upstream-name . "GenomicFiles"))) (build-system r-build-system) (propagated-inputs @@ -10105,14 +10208,14 @@ provide added flexibility for data combination and manipulation.") (define-public r-complexheatmap (package (name "r-complexheatmap") - (version "2.2.0") + (version "2.4.2") (source (origin (method url-fetch) (uri (bioconductor-uri "ComplexHeatmap" version)) (sha256 (base32 - "1pj6a6rmqckk033pkklk6hr4066rzavamy6w194rfdhind90rk0p")))) + "01jxxwxhf9n8baxgja4rb592p5210s4ppd7a5b4xby5aalhzkr0l")))) (properties `((upstream-name . "ComplexHeatmap"))) (build-system r-build-system) @@ -10124,6 +10227,8 @@ provide added flexibility for data combination and manipulation.") ("r-globaloptions" ,r-globaloptions) ("r-png" ,r-png) ("r-rcolorbrewer" ,r-rcolorbrewer))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/jokergoo/ComplexHeatmap") (synopsis "Making Complex Heatmaps") @@ -10137,14 +10242,14 @@ self-defined annotation graphics.") (define-public r-dirichletmultinomial (package (name "r-dirichletmultinomial") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DirichletMultinomial" version)) (sha256 (base32 - "0knmncmkkf2ypyqfcl5s8nmyyf9nrzkqprzn9w3w8182c0v49r0s")))) + "1m9dsrddrllb2i88qzik1867iv9mggrgdkn0dlp8sq7gl69vmalb")))) (properties `((upstream-name . "DirichletMultinomial"))) (build-system r-build-system) @@ -10166,14 +10271,14 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): (define-public r-ensembldb (package (name "r-ensembldb") - (version "2.10.2") + (version "2.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ensembldb" version)) (sha256 (base32 - "02lnpyp85zchmz404hr5381zmihvq4x9zgxdrbn2afi352vg0vab")))) + "1vvchc04nshxc768fp31rxb603aj3hmq8xlh5qabcwf2c3z9719g")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -10192,6 +10297,8 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): ("r-rsqlite" ,r-rsqlite) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/jotsetung/ensembldb") (synopsis "Utilities to create and use Ensembl-based annotation databases") (description @@ -10209,14 +10316,14 @@ chromosome region or transcript models of lincRNA genes.") (define-public r-organismdbi (package (name "r-organismdbi") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "OrganismDbi" version)) (sha256 (base32 - "1bvfyh733mhka9zd00hrzpalgjs255c2blnxyf60ipzk5jg7yllb")))) + "194h5576inq44qr666snzq0ygnc77rk5ljkn9bn8zs6x6gb3cwaw")))) (properties `((upstream-name . "OrganismDbi"))) (build-system r-build-system) (propagated-inputs @@ -10241,14 +10348,14 @@ the fact that each of these packages implements a select methods.") (define-public r-biovizbase (package (name "r-biovizbase") - (version "1.34.1") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biovizBase" version)) (sha256 (base32 - "04vvj907bgs67w8rb7n1haf80p6cd0qj5fdxw0dwryb455y35vir")))) + "1vq2mxa2jkljgw75zqjdkyml0ppi5dspvwj4cznfhi31cq8ds0qh")))) (properties `((upstream-name . "biovizBase"))) (build-system r-build-system) (propagated-inputs @@ -10283,14 +10390,14 @@ effort and encourages consistency.") (define-public r-ggbio (package (name "r-ggbio") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggbio" version)) (sha256 (base32 - "13wzwh40anh8l53yp19bg4w5cpxykcaf228dc8cxvjndyib711qb")))) + "11ggnqjq42fi2hm9xlvrrlr2xhy4kglvl1a0mycp1s4v67lxw5h5")))) (build-system r-build-system) (arguments `(#:phases @@ -10330,6 +10437,8 @@ effort and encourages consistency.") ("r-scales" ,r-scales) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-variantannotation" ,r-variantannotation))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "http://www.tengfei.name/ggbio/") (synopsis "Visualization tools for genomic data") (description @@ -10343,41 +10452,17 @@ views. High-level plots include sequence fragment length, edge-linked interval to data view, mismatch pileup, and several splicing summaries.") (license license:artistic2.0))) -(define-public r-gprofiler - (package - (name "r-gprofiler") - (version "0.7.0") - (source - (origin - (method url-fetch) - (uri (cran-uri "gProfileR" version)) - (sha256 - (base32 - "1h1v0kgpsn04ald2izznh7fr2riwisj5hcgz4k7h3qc931rf0r4k")))) - (properties `((upstream-name . "gProfileR"))) - (build-system r-build-system) - (propagated-inputs - `(("r-plyr" ,r-plyr) - ("r-rcurl" ,r-rcurl))) - (home-page "https://cran.r-project.org/web/packages/gProfileR/") - (synopsis "Interface to the g:Profiler toolkit") - (description - "This package provides tools for functional enrichment analysis, -gene identifier conversion and mapping homologous genes across related -organisms via the @code{g:Profiler} toolkit.") - (license license:gpl2+))) - (define-public r-gqtlbase (package (name "r-gqtlbase") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gQTLBase" version)) (sha256 (base32 - "1qr8dqjbmj1mdjbzbnxwzfrm8f02wqfsgic8ws5kv7pmsby63y4x")))) + "06xvzp4fn3qfa46ggg8kxi267gbyd821vvx4040173xkqxpr0g5j")))) (properties `((upstream-name . "gQTLBase"))) (build-system r-build-system) (propagated-inputs @@ -10394,6 +10479,8 @@ organisms via the @code{g:Profiler} toolkit.") ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors) ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/gQTLBase") (synopsis "Infrastructure for eQTL, mQTL and similar studies") (description @@ -10405,14 +10492,14 @@ and more.") (define-public r-snpstats (package (name "r-snpstats") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "snpStats" version)) (sha256 (base32 - "1xq1rjljg70h5mshdza56dis0iv1a20sivs6dav3w5jbdd1l5qkh")))) + "1qv3nqqr30d3n66mawqd9dbl95dl89r4bcjvkc5iassy1yrwr8wq")))) (properties `((upstream-name . "snpStats"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) @@ -10464,14 +10551,14 @@ several related annotation packages.") (define-public r-erma (package (name "r-erma") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "erma" version)) (sha256 (base32 - "085qsr73p8nyp435f15l4l1jkfd64bfd9gl4z496nfxdnqn95srz")))) + "1ccfbq0r48sr3h8050w8zv8402h7nx09adr0xdyqlg7kwp9vd2l3")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -10488,6 +10575,8 @@ several related annotation packages.") ("r-s4vectors" ,r-s4vectors) ("r-shiny" ,r-shiny) ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/erma") (synopsis "Epigenomic road map adventures") (description @@ -10502,14 +10591,14 @@ by Ernst and Kellis.") (define-public r-ldblock (package (name "r-ldblock") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ldblock" version)) (sha256 (base32 - "0xpigfidmylfawy6vzshqnsw1lzjs4qms8q7zffij6bkvkv7920x")))) + "0plw00n2zfgh029ab41dnydzgv2yxrapjp770147rx9pff4dngrv")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -10522,6 +10611,8 @@ by Ernst and Kellis.") ("r-rsamtools" ,r-rsamtools) ("r-snpstats" ,r-snpstats) ("r-variantannotation" ,r-variantannotation))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/ldblock") (synopsis "Data structures for linkage disequilibrium measures in populations") (description @@ -10534,14 +10625,14 @@ defining LD blocks.") (define-public r-gqtlstats (package (name "r-gqtlstats") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gQTLstats" version)) (sha256 (base32 - "1dly4p9r4231hf31xg1nzqiyvjbcfjljfmhb88ic1jxwnvniyv2f")))) + "1jjqfpjp93nmxjn757j5mzcax96bzcqdd1gr3rsdxg7ap008l2w7")))) (properties `((upstream-name . "gQTLstats"))) (build-system r-build-system) (propagated-inputs @@ -10575,6 +10666,8 @@ defining LD blocks.") ("r-snpstats" ,r-snpstats) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-variantannotation" ,r-variantannotation))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/gQTLstats") (synopsis "Computationally efficient analysis for eQTL and allied studies") (description @@ -10588,14 +10681,14 @@ family of feature/genome hypotheses.") (define-public r-gviz (package (name "r-gviz") - (version "1.30.3") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Gviz" version)) (sha256 (base32 - "0c9i26h5czm60n1bxzmdxxpywcj0sig6wcj913pb41mr83bbgra3")))) + "0cgkp0ciyy2qykqgh3vzp5mx9b4vsvacjh2jnsj3wldiapzlz08a")))) (properties `((upstream-name . "Gviz"))) (build-system r-build-system) (propagated-inputs @@ -10607,6 +10700,7 @@ family of feature/genome hypotheses.") ("r-biovizbase" ,r-biovizbase) ("r-bsgenome" ,r-bsgenome) ("r-digest" ,r-digest) + ("r-ensembldb" ,r-ensembldb) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicalignments" ,r-genomicalignments) ("r-genomicfeatures" ,r-genomicfeatures) @@ -10620,6 +10714,8 @@ family of feature/genome hypotheses.") ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors) ("r-xvector" ,r-xvector))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/Gviz") (synopsis "Plotting data and annotation information along genomic coordinates") (description @@ -10634,14 +10730,14 @@ with your data.") (define-public r-gwascat (package (name "r-gwascat") - (version "2.18.0") + (version "2.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "gwascat" version)) (sha256 (base32 - "038vhfsk2vs7inn5di093cmjbb81k7j0af385sg7l01jj70bdqq1")))) + "1cq5cmdrf0a0arr841yvkh6d8drc15p7mif1afr215l1s3y2dwd4")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -10650,11 +10746,13 @@ with your data.") ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) - ("r-homo-sapiens" ,r-homo-sapiens) + ("r-ggplot2" ,r-ggplot2) ("r-iranges" ,r-iranges) ("r-rsamtools" ,r-rsamtools) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/gwascat") (synopsis "Tools for data in the EMBL-EBI GWAS catalog") (description @@ -10665,13 +10763,13 @@ EMBL-EBI GWAS catalog.") (define-public r-sushi (package (name "r-sushi") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Sushi" version)) (sha256 (base32 - "15xng21hd09fb234ravrry3b872zg82w8x9lijxab9n96xihcpz5")))) + "17j3d5qjq5nbv99by5mq8rwr0jgh2jyyfn2nwxmwgzlmk3lgi1rb")))) (properties `((upstream-name . "Sushi"))) (build-system r-build-system) (propagated-inputs @@ -10687,19 +10785,21 @@ visualizations for publication-quality multi-panel figures.") (define-public r-fithic (package (name "r-fithic") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FitHiC" version)) (sha256 (base32 - "1irwkwi4afdj395134k31mvx7c2vpdd0rv8zrblnldascdsb04kc")))) + "1dffkdxm08wq4kjd9j2v2625x3p6vbrk33a2zx94pwpgkghr72yp")))) (properties `((upstream-name . "FitHiC"))) (build-system r-build-system) (propagated-inputs `(("r-data-table" ,r-data-table) ("r-fdrtool" ,r-fdrtool) ("r-rcpp" ,r-rcpp))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/FitHiC") (synopsis "Confidence estimation for intra-chromosomal contact maps") (description @@ -10711,13 +10811,13 @@ assays such as Hi-C.") (define-public r-hitc (package (name "r-hitc") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HiTC" version)) (sha256 (base32 - "0byahi0fz0dzjyklz8v9whax9ygg7gwb4pl1j3zbl6z8a9qx8pps")))) + "1jx2pfa7sbdz7xi466lz1h5xv126g56z73n0a5l2wrq28k47qaxy")))) (properties `((upstream-name . "HiTC"))) (build-system r-build-system) (propagated-inputs @@ -10740,14 +10840,14 @@ provided.") (define-public r-hdf5array (package (name "r-hdf5array") - (version "1.14.4") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HDF5Array" version)) (sha256 (base32 - "0ib0grhd9zbrn0dkrm4aa7qj7h0y6z1dvyx1ab3w6vczw7xghsfb")))) + "1g848s0qc6i4ipd7y2s5pk8k1xggk2kfy0gnr8wjjs2gq3914aw4")))) (properties `((upstream-name . "HDF5Array"))) (build-system r-build-system) (inputs @@ -10770,19 +10870,22 @@ block processing.") (define-public r-rhdf5lib (package (name "r-rhdf5lib") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhdf5lib" version)) (sha256 (base32 - "17lhwnm9rqsvbqkvwp0m07vjrk63a4389p2y39zffv8fgznxqzd7")) + "09ylwyk6a8sdrmi1mx7vpycpykqlqylmwa973g6jrcmk0h0qfa4w")) (modules '((guix build utils))) (snippet '(begin ;; Delete bundled binaries - (delete-file-recursively "src/winlib/") + (delete-file-recursively "src/wininclude/") + (delete-file-recursively "src/winlib-4.9.3/") + (delete-file-recursively "src/winlib-8.3.0/") + (delete-file "src/hdf5small_cxx_hl_1.10.6.tar.gz") #t)))) (properties `((upstream-name . "Rhdf5lib"))) (build-system r-build-system) @@ -10818,6 +10921,8 @@ block processing.") "C Compiler: GCC\n")) (rename-file "Makevars.in" "Makevars") (substitute* "Makevars" + (("@ZLIB_LIB@") "-lz") + (("@ZLIB_INCLUDE@") "") (("HDF5_CXX_LIB=.*") (string-append "HDF5_CXX_LIB=" (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n")) @@ -10843,7 +10948,8 @@ block processing.") (propagated-inputs `(("hdf5" ,hdf5-1.10))) (native-inputs - `(("hdf5-source" ,(package-source hdf5-1.10)))) + `(("hdf5-source" ,(package-source hdf5-1.10)) + ("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/Rhdf5lib") (synopsis "HDF5 library as an R package") (description "This package provides C and C++ HDF5 libraries for use in R @@ -10853,19 +10959,21 @@ packages.") (define-public r-beachmat (package (name "r-beachmat") - (version "2.2.1") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "beachmat" version)) (sha256 (base32 - "1bpnlw2kdy9yc2vq948k980r0j25ipb80llhvn0j3kxjiwyfgs3i")))) + "1vl6jbf9ia78cm4ikdb8vz04jv4b46zhvg5i006c63a9pzw7zhxi")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-delayedarray" ,r-delayedarray) ("r-matrix" ,r-matrix))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/beachmat") (synopsis "Compiling Bioconductor to handle each matrix type") (description "This package provides a consistent C++ class interface for a @@ -10876,14 +10984,14 @@ matrices.") (define-public r-singlecellexperiment (package (name "r-singlecellexperiment") - (version "1.8.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "SingleCellExperiment" version)) (sha256 (base32 - "11pqb3cigi9xbhxq2k3n7z23v1ibd03ws1lcrh5c5ffgb33nlyw5")))) + "092wvk11n7pa234vlwhxm3gdi4k3sbnz1splhxalbdhz3jf02zfp")))) (properties `((upstream-name . "SingleCellExperiment"))) (build-system r-build-system) @@ -10891,6 +10999,8 @@ matrices.") `(("r-biocgenerics" ,r-biocgenerics) ("r-s4vectors" ,r-s4vectors) ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/SingleCellExperiment") (synopsis "S4 classes for single cell data") (description "This package defines an S4 class for storing data from @@ -10903,13 +11013,13 @@ libraries.") (define-public r-scater (package (name "r-scater") - (version "1.14.6") + (version "1.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "scater" version)) (sha256 (base32 - "0sxd1s8wdlj9926bagq4crjrk1nnmh3j3bhgrw160zfgc3y8pzck")))) + "0pi4mpc3lvskj5biyhc9cskcnz9q2wjmfrz7xdnx8qqd8vpy84g3")))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) @@ -10923,10 +11033,13 @@ libraries.") ("r-ggplot2" ,r-ggplot2) ("r-matrix" ,r-matrix) ("r-rcpp" ,r-rcpp) + ("r-rlang" ,r-rlang) ("r-s4vectors" ,r-s4vectors) ("r-singlecellexperiment" ,r-singlecellexperiment) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-viridis" ,r-viridis))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/davismcc/scater") (synopsis "Single-cell analysis toolkit for gene expression data in R") (description "This package provides a collection of tools for doing @@ -10937,14 +11050,14 @@ quality control.") (define-public r-scran (package (name "r-scran") - (version "1.14.6") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scran" version)) (sha256 (base32 - "1y8wlgk5zbv7c7gcp0ahfpbh9lifab7y3zwf0093fzaw7vr1y6cr")))) + "1gm4ys4aq8h1pn45k1rxk384wjyf55izivw8kgxbrflj6j4xvvsv")))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) @@ -10958,6 +11071,7 @@ quality control.") ("r-dqrng" ,r-dqrng) ("r-edger" ,r-edger) ("r-igraph" ,r-igraph) + ("r-iranges" ,r-iranges) ("r-limma" ,r-limma) ("r-matrix" ,r-matrix) ("r-rcpp" ,r-rcpp) @@ -10966,6 +11080,8 @@ quality control.") ("r-singlecellexperiment" ,r-singlecellexperiment) ("r-statmod" ,r-statmod) ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/scran") (synopsis "Methods for single-cell RNA-Seq data analysis") (description "This package implements a variety of low-level analyses of @@ -10977,14 +11093,14 @@ variable and significantly correlated genes.") (define-public r-delayedmatrixstats (package (name "r-delayedmatrixstats") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedMatrixStats" version)) (sha256 (base32 - "0mv2rl6a6l404piabcazxz1s6ars016pxhjf5v40hhr6y1r0wbqy")))) + "0i6gw8058gw9yajya3w9qq6l3p634fq9sv8dh8ifigxz0k9b98r6")))) (properties `((upstream-name . "DelayedMatrixStats"))) (build-system r-build-system) @@ -10996,6 +11112,8 @@ variable and significantly correlated genes.") ("r-matrix" ,r-matrix) ("r-matrixstats" ,r-matrixstats) ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/PeteHaitch/DelayedMatrixStats") (synopsis "Functions that apply to rows and columns of DelayedMatrix objects") (description @@ -13738,18 +13856,31 @@ bound.") (define-public python-pypairix (package (name "python-pypairix") - (version "0.3.6") + (version "0.3.7") + ;; The tarball on pypi does not include the makefile to build the + ;; programs. (source (origin - (method url-fetch) - (uri (pypi-uri "pypairix" version)) + (method git-fetch) + (uri (git-reference + (url "https://github.com/4dn-dcic/pairix.git") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "0zs92b74s5v4xy2h16s15f3z6l4nnbw8x8zyif7xx5xpafjn0xss")))) + "1snr3lrmsld8sy77ng6ba6wcmd33xjccf1l2f3m6pi29xis9nd6p")))) (build-system python-build-system) - ;; FIXME: the tests fail because test.support cannot be loaded: - ;; ImportError: cannot import name 'support' - (arguments '(#:tests? #f)) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'build 'build-programs + (lambda _ (invoke "make"))) + (add-after 'install 'install-programs + (lambda* (#:key outputs #:allow-other-keys) + (copy-recursively "bin" (string-append + (assoc-ref outputs "out") + "/bin")) + #t))))) (inputs `(("zlib" ,zlib))) (home-page "https://github.com/4dn-dcic/pairix") @@ -14679,7 +14810,7 @@ is a Cython wrapper for FIt-SNE.") ("java-eclipse-jdt-core" ,java-eclipse-jdt-core) ("java-eclipse-jdt-compiler-apt" ,java-eclipse-jdt-compiler-apt) ("java-openmpi" ,java-openmpi))) - (home-page "http://sourceforge.net/projects/bbmap/") + (home-page "https://sourceforge.net/projects/bbmap/") (synopsis "Aligner and other tools for short sequencing reads") (description "This package provides bioinformatic tools to align, deduplicate, |