diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 111 |
1 files changed, 74 insertions, 37 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b191c8b4ae..73d5fe37eb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -798,14 +798,14 @@ closely reconstructs the mutational profile.") (define-public r-nmf (package (name "r-nmf") - (version "0.22.0") + (version "0.23.0") (source (origin (method url-fetch) (uri (cran-uri "NMF" version)) (sha256 (base32 - "0b2ls3x1nkrnam45hagpys624nzxj3v7kxnp0q216yakvx5h57cq")))) + "0ls7q9yc9l1z10jphq5a11wkfgcxc3gm3sfjj376zx3vnc0wl30g")))) (properties `((upstream-name . "NMF"))) (build-system r-build-system) (propagated-inputs @@ -826,6 +826,8 @@ closely reconstructs the mutational profile.") ("r-reshape2" ,r-reshape2) ("r-rngtools" ,r-rngtools) ("r-stringr" ,r-stringr))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "http://renozao.github.io/NMF") (synopsis "Algorithms and framework for nonnegative matrix factorization") (description @@ -1502,14 +1504,14 @@ browser.") (define-public r-oligoclasses (package (name "r-oligoclasses") - (version "1.50.0") + (version "1.50.4") (source (origin (method url-fetch) (uri (bioconductor-uri "oligoClasses" version)) (sha256 (base32 - "05jy9qz3ir4maxackr1xqlfi1czhy1qd22wwibjdhfh5dp534cpn")))) + "1d8c3i8v8kcm1afgpz6zc1iysip7993y8456cqxl37f7n6n0ax67")))) (properties `((upstream-name . "oligoClasses"))) (build-system r-build-system) (propagated-inputs @@ -1537,14 +1539,14 @@ packages.") (define-public r-oligo (package (name "r-oligo") - (version "1.52.0") + (version "1.52.1") (source (origin (method url-fetch) (uri (bioconductor-uri "oligo" version)) (sha256 (base32 - "102szyiicws4c6l3k282236ml1m1vl9zmars4q1kdjfnvsyclfc4")))) + "1gpvr33pwzz1glzajcipvjcplb7yxvjj00q0ybqcc3wa47bhfkwd")))) (properties `((upstream-name . "oligo"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) @@ -1791,14 +1793,14 @@ determining dependencies between variables, code improvement suggestions.") (define-public r-chippeakanno (package (name "r-chippeakanno") - (version "3.22.2") + (version "3.22.3") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPpeakAnno" version)) (sha256 (base32 - "199mlg0gwjy39afyk0ah6lzcm759bzxla4hgcajj0ay9jiibjqpa")))) + "0q3f55hh0a2hl96272js6gagmgps9cxs8s13pf6fii64rzaz5m7y")))) (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs @@ -3450,14 +3452,14 @@ surface of a flowcell.") (define-public r-gkmsvm (package (name "r-gkmsvm") - (version "0.80.0") + (version "0.81.0") (source (origin (method url-fetch) (uri (cran-uri "gkmSVM" version)) (sha256 (base32 - "0ljcga246ad0ql8x3drvrdsyp0f20mgp3p6lnl79xb76qgfdnm0p")))) + "119g5rhc7ffyviz04r04aj5z1g6abnj3ddd01g7db505sdr6lapj")))) (properties `((upstream-name . "gkmSVM"))) (build-system r-build-system) (propagated-inputs @@ -3622,14 +3624,14 @@ information about samples and features can be added to the plot.") (define-public r-gosemsim (package (name "r-gosemsim") - (version "2.14.0") + (version "2.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GOSemSim" version)) (sha256 (base32 - "0mg4d8whq90iyl2jjj5dx3kyar17yqn00jvia3b4a8lhmjw8l1hk")))) + "0v4q9xr1cm5xr08pgbzrss41kh3yz7xyh31n55l0sjmr1629ykln")))) (properties `((upstream-name . "GOSemSim"))) (build-system r-build-system) (propagated-inputs @@ -3810,14 +3812,14 @@ All the visualization methods are developed based on ggplot2 graphics.") (define-public r-clusterprofiler (package (name "r-clusterprofiler") - (version "3.16.0") + (version "3.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterProfiler" version)) (sha256 (base32 - "0m7919gzrd2fddb4kcznwpshhab1ha2yppnkxg11zmh40wcdawyi")))) + "11zsgb8wbdv8r4c04iczz4aala4yw4ai7rz8igdzz87c0940nxkb")))) (properties `((upstream-name . "clusterProfiler"))) (build-system r-build-system) @@ -3832,6 +3834,7 @@ All the visualization methods are developed based on ggplot2 graphics.") ("r-magrittr" ,r-magrittr) ("r-plyr" ,r-plyr) ("r-qvalue" ,r-qvalue) + ("r-rlang" ,r-rlang) ("r-rvcheck" ,r-rvcheck) ("r-tidyr" ,r-tidyr))) (native-inputs @@ -4087,7 +4090,8 @@ Affymetrix arrays.") (properties `((upstream-name . "abseqR"))) (build-system r-build-system) (inputs - `(("pandoc" ,ghc-pandoc))) + `(("pandoc" ,pandoc) + ("pandoc-citeproc" ,pandoc-citeproc))) (propagated-inputs `(("r-biocparallel" ,r-biocparallel) ("r-biocstyle" ,r-biocstyle) @@ -4287,14 +4291,14 @@ Bioconductor.") (define-public r-motifstack (package (name "r-motifstack") - (version "1.32.0") + (version "1.32.1") (source (origin (method url-fetch) (uri (bioconductor-uri "motifStack" version)) (sha256 (base32 - "008f2mjcyyiz84ilrsldpqwvxy2lp93hjggrq4nrqwi78nyx3ls5")))) + "02vmkgn36n5xpmizy33znlzgmi3w5hnhsibgisbnhwwgxpkrwpcd")))) (properties `((upstream-name . "motifStack"))) (build-system r-build-system) (propagated-inputs @@ -4356,14 +4360,14 @@ position-specific scores within R and Bioconductor.") (define-public r-atacseqqc (package (name "r-atacseqqc") - (version "1.12.3") + (version "1.12.4") (source (origin (method url-fetch) (uri (bioconductor-uri "ATACseqQC" version)) (sha256 (base32 - "12710c4024pndwwqiiqr6dhrd360z26fc8r3fxhs739gyd0ddk9r")))) + "1gs9862hhh4gr1akij6ykhcj29s9dzg1vnj87hqrm19dfgl43qbh")))) (properties `((upstream-name . "ATACseqQC"))) (build-system r-build-system) (propagated-inputs @@ -5236,14 +5240,14 @@ This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID (define-public r-rbowtie2 (package (name "r-rbowtie2") - (version "1.10.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie2" version)) (sha256 (base32 - "1z2dn0q3wcw8b9ibx388kh7p5km16i71sw9miqj3daw7g0v5bxp3")))) + "19v7wfvrd53j618c1xbiqnlsf2kxw697myryx0vb9s2aspknyzz7")))) (properties `((upstream-name . "Rbowtie2"))) (build-system r-build-system) (inputs @@ -5314,14 +5318,14 @@ Infinium HumanMethylation 450k assay.") (define-public r-biocfilecache (package (name "r-biocfilecache") - (version "1.12.0") + (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocFileCache" version)) (sha256 (base32 - "02chrzwccmazi7rdfpyriizhbgxyxlmprlw32w05wk54as6wrxv8")))) + "02yayjyliaqxcwqa0n2ccmsfflskqzf0gvdibh2r3nz5bi66imkf")))) (properties `((upstream-name . "BiocFileCache"))) (build-system r-build-system) (propagated-inputs @@ -5376,14 +5380,14 @@ Gaussian distributions.") (define-public r-rbowtie (package (name "r-rbowtie") - (version "1.28.0") + (version "1.28.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie" version)) (sha256 (base32 - "06y1qp915dlwjdi2fs3344sgya55pcv07f3i61y0cxb0bhbcgvrz")))) + "0589ggbfx6di42wvqyhnzgrhmb52swr3r5z22w6b8x0z2y7hl8b3")))) (properties `((upstream-name . "Rbowtie"))) (build-system r-build-system) (inputs @@ -5781,14 +5785,14 @@ annotations.") (define-public r-rsubread (package (name "r-rsubread") - (version "2.2.4") + (version "2.2.6") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 - "0yznfqgp5cbz68n3rrfvm752267da16kl538zdrb1g1aw9zdfqc6")))) + "04h79qhq93d8id0rr5xnj9vf82ygwxzdlnck78yv738xd0jjvnpm")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) @@ -6330,14 +6334,14 @@ self-organizing map clustering and minimal spanning trees.") (define-public r-mixomics (package (name "r-mixomics") - (version "6.12.1") + (version "6.12.2") (source (origin (method url-fetch) (uri (bioconductor-uri "mixOmics" version)) (sha256 (base32 - "13kq9l5xwhwp30y5gfqfh5f11n63vn8rk195mb2y2mww4cwi6lv4")))) + "1nkqlvm9j1f4vfj3f3kyxqgan38rpa9imimvl9pwivvsfl647vvc")))) (properties `((upstream-name . "mixOmics"))) (build-system r-build-system) (propagated-inputs @@ -6456,14 +6460,14 @@ genes in the gene-set that are ranked above the leading edge).") (define-public r-cicero (package (name "r-cicero") - (version "1.6.1") + (version "1.6.2") (source (origin (method url-fetch) (uri (bioconductor-uri "cicero" version)) (sha256 (base32 - "0nf9yqg5krj26n4n82iyx3rsr84d46b17i9zfk35sh12l4xssbii")))) + "042ba6yfa7fksij2v7cwnp2sca3vmz7izn6fsxx9xswnncrkgcqh")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) @@ -7048,14 +7052,14 @@ arrays based on fast wavelet-based functional models.") (define-public r-variancepartition (package (name "r-variancepartition") - (version "1.18.2") + (version "1.18.3") (source (origin (method url-fetch) (uri (bioconductor-uri "variancePartition" version)) (sha256 (base32 - "19bhkb8vd44m3nkznw075fx3y2p3a1bsazbhcfiqw9n4190k9bgv")))) + "1jrlhi2c5ibvq8a41g5hwdq4kk4rdd7m464rz5767zaaci7l2ay0")))) (properties `((upstream-name . "variancePartition"))) (build-system r-build-system) @@ -7762,14 +7766,14 @@ different graph related packages produced by Bioconductor.") (define-public r-experimenthub (package (name "r-experimenthub") - (version "1.14.0") + (version "1.14.2") (source (origin (method url-fetch) (uri (bioconductor-uri "ExperimentHub" version)) (sha256 (base32 - "18d6kjfavy5b769gpkblihdkz2nz2hsgyjki8mp1sywi0ik08ncd")))) + "1kgvprchz1fg8pl1irj62mk2gyb4jcc9iimpypv4c2iccy5bp84x")))) (properties `((upstream-name . "ExperimentHub"))) (build-system r-build-system) (propagated-inputs @@ -7955,14 +7959,14 @@ analytics on packages.") (define-public r-biocset (package (name "r-biocset") - (version "1.2.1") + (version "1.2.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocSet" version)) (sha256 (base32 - "14dmkc878lskbm001kgjyqmrwnn6s032z4h64f617f1xd9zx9wrj")))) + "041hq3rp0kv7kjwcjjrksk8lw3sj6j1v3wdcr8z611k0g0z6p0cj")))) (properties `((upstream-name . "BiocSet"))) (build-system r-build-system) (propagated-inputs @@ -8116,3 +8120,36 @@ dimensional mass cytometry data.") Tool) analysis automatic by constructing a HTTP POST request according to user's input and automatically retrieving results from GREAT web server.") (license license:expat))) + +(define-public r-m3c + (package + (name "r-m3c") + (version "1.10.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "M3C" version)) + (sha256 + (base32 + "0zq8lm4280p8h65i7myscwa4srs5ajh944xv6zni2f5sjyp7ij2y")))) + (properties `((upstream-name . "M3C"))) + (build-system r-build-system) + (propagated-inputs + `(("r-cluster" ,r-cluster) + ("r-corpcor" ,r-corpcor) + ("r-doparallel" ,r-doparallel) + ("r-dosnow" ,r-dosnow) + ("r-foreach" ,r-foreach) + ("r-ggplot2" ,r-ggplot2) + ("r-matrix" ,r-matrix) + ("r-matrixcalc" ,r-matrixcalc) + ("r-rtsne" ,r-rtsne) + ("r-umap" ,r-umap))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/M3C") + (synopsis "Monte Carlo reference-based consensus clustering") + (description + "M3C is a consensus clustering algorithm that uses a Monte Carlo +simulation to eliminate overestimation of @code{K} and can reject the null +hypothesis @code{K=1}.") + (license license:agpl3+))) |