diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 45 |
1 files changed, 22 insertions, 23 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 065555b37b..4adb3137e5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2744,7 +2744,7 @@ quantitative phenotypes.") (define-public edirect (package (name "edirect") - (version "12.1.20190819") + (version "12.1.20190829") (source (origin (method url-fetch) (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect" @@ -2752,7 +2752,7 @@ quantitative phenotypes.") "/edirect-" version ".tar.gz")) (sha256 (base32 - "1i9s9mppcfqd60pfywpm8vdyz5vpnyslw22nd7dv0bhykrdnkz9g")))) + "1xb330z28dgp7slrvp8r7rgncsasv9lpcpqim571yg728dq7xdik")))) (build-system perl-build-system) (arguments `(#:phases @@ -6935,14 +6935,14 @@ testing and other simple calculations.") (define-public r-shortread (package (name "r-shortread") - (version "1.44.1") + (version "1.44.3") (source (origin (method url-fetch) (uri (bioconductor-uri "ShortRead" version)) (sha256 (base32 - "1dh3q83hmi4l72vpif6dn51dzbi9ljrjgkq2zxg4sqy2jxv4vwza")))) + "0ykyrj4g6vc67d5s46sp4659qvar2iavflzhggm79w4p50hxia4s")))) (properties `((upstream-name . "ShortRead"))) (build-system r-build-system) (inputs @@ -7532,13 +7532,13 @@ coding changes and predict coding outcomes.") (define-public r-limma (package (name "r-limma") - (version "3.42.0") + (version "3.42.2") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "0cfynv6qbnar5rl7vjh5lvddd381g9wqx1zd6a7l130hf59mwswn")))) + "1nd01r7rd7jb5qz84vbgfnyrmgm9wiq7fsdji68537kjgvrzmm9z")))) (build-system r-build-system) (home-page "http://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") @@ -7751,13 +7751,13 @@ biological sequences or sets of sequences.") (define-public r-rsamtools (package (name "r-rsamtools") - (version "2.2.1") + (version "2.2.2") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsamtools" version)) (sha256 (base32 - "0hpdc88prpq1gcja89n5s1ndcg81523qrkbkm9gbhm7rm8wmi8cl")))) + "1larx1a9cngmcsm2n7yyxrlnk69zi8m9dp3b90jva0ynspyi76v7")))) (properties `((upstream-name . "Rsamtools"))) (build-system r-build-system) @@ -7939,13 +7939,13 @@ as well as query and modify the browser state, such as the current viewport.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.38.1") + (version "1.38.2") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "1c1x29f447dv0i1wi88paji645lfsgmg4ckn19hyhlra72smhzqc")))) + "0dd226kgks50jdx5w35f3wmg95hy8aibi4kcn8p5kmqp5i8j580b")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) @@ -8236,7 +8236,7 @@ throughput genetic sequencing data sets using regression methods.") (define-public r-qtl (package (name "r-qtl") - (version "1.44-9") + (version "1.45-11") (source (origin (method url-fetch) @@ -8244,7 +8244,7 @@ throughput genetic sequencing data sets using regression methods.") version ".tar.gz")) (sha256 (base32 - "03lmvydln8b7666b6w46qbryhf83vsd11d4y2v95rfgvqgq66l1i")))) + "1d6qgj602fm6zia3djl4hmca0ri4v57ffp3g93p2yc3cabx2hq90")))) (build-system r-build-system) (home-page "https://rqtl.org/") (synopsis "R package for analyzing QTL experiments in genetics") @@ -8332,14 +8332,14 @@ secondary structure and comparative analysis in R.") (define-public r-rhtslib (package (name "r-rhtslib") - (version "1.18.0") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhtslib" version)) (sha256 (base32 - "04inkq44lxwymqv51mxgaphasqjcdc9rl5p58imnrdm0kszs8prm")))) + "0gkbrmrcg55c9s5166ifljlx0v25rv4ijdyp4wf4c292xd6chy2l")))) (properties `((upstream-name . "Rhtslib"))) (build-system r-build-system) ;; Without this a temporary directory ends up in the Rhtslib.so binary, @@ -9504,13 +9504,13 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.") (define-public r-seurat (package (name "r-seurat") - (version "3.1.2") + (version "3.1.3") (source (origin (method url-fetch) (uri (cran-uri "Seurat" version)) (sha256 (base32 - "0m1qi39snbmkkv1p07bzg1r7snc9x6a1y0dghvpk1nzgcfpmnsj4")))) + "0962mfgqk1di3wy1j0xdkvnw0q5m3q4xzd67d1l6dijlqiz8nfal")))) (properties `((upstream-name . "Seurat"))) (build-system r-build-system) (propagated-inputs @@ -9549,7 +9549,6 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.") ("r-rtsne" ,r-rtsne) ("r-scales" ,r-scales) ("r-sctransform" ,r-sctransform) - ("r-sdmtools" ,r-sdmtools) ("r-tsne" ,r-tsne) ("r-uwot" ,r-uwot))) (home-page "http://www.satijalab.org/seurat") @@ -10326,14 +10325,14 @@ family of feature/genome hypotheses.") (define-public r-gviz (package (name "r-gviz") - (version "1.30.1") + (version "1.30.3") (source (origin (method url-fetch) (uri (bioconductor-uri "Gviz" version)) (sha256 (base32 - "03jj193fzmhvkjw8f5zk6wgflkvm3phny0q38scawcplfsyb8z64")))) + "0c9i26h5czm60n1bxzmdxxpywcj0sig6wcj913pb41mr83bbgra3")))) (properties `((upstream-name . "Gviz"))) (build-system r-build-system) (propagated-inputs @@ -10478,14 +10477,14 @@ provided.") (define-public r-hdf5array (package (name "r-hdf5array") - (version "1.14.1") + (version "1.14.2") (source (origin (method url-fetch) (uri (bioconductor-uri "HDF5Array" version)) (sha256 (base32 - "04hd02zd5jix5p2zg10asmwjg1fynqgmclbhbmk7fb6arx5hm11f")))) + "0mbx9rsr2571k4k4hmx3dr49rhqb31dhwy2r2bkrd4dbhvriqgld")))) (properties `((upstream-name . "HDF5Array"))) (build-system r-build-system) (inputs @@ -10675,14 +10674,14 @@ quality control.") (define-public r-scran (package (name "r-scran") - (version "1.14.5") + (version "1.14.6") (source (origin (method url-fetch) (uri (bioconductor-uri "scran" version)) (sha256 (base32 - "0ydy6gvpgpvrs4ryk1qvmmxp6cpaizs294jwg42jawxndkds1l3y")))) + "1y8wlgk5zbv7c7gcp0ahfpbh9lifab7y3zwf0093fzaw7vr1y6cr")))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) |