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* gnu: r-genomicranges: Update to 1.30.0.•••* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.30.0. Ricardo Wurmus2017-11-07
* gnu: r-xvector: Update to 0.18.0.•••* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.18.0. Ricardo Wurmus2017-11-07
* gnu: r-limma: Update to 3.34.0.•••* gnu/packages/bioinformatics.scm (r-limma): Update to 3.34.0. Ricardo Wurmus2017-11-07
* gnu: r-variantannotation: Update to 1.24.0.•••* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.24.0. Ricardo Wurmus2017-11-07
* gnu: r-genomeinfodb: Update to 1.14.0.•••* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.14.0. Ricardo Wurmus2017-11-07
* gnu: r-iranges: Update to 2.12.0.•••* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.12.0. Ricardo Wurmus2017-11-07
* gnu: r-s4vectors: Update to 0.16.0.•••* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.16.0. Ricardo Wurmus2017-11-07
* gnu: r-biocstyle: Update to 2.6.0.•••* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.6.0. Ricardo Wurmus2017-11-07
* gnu: r-biocinstaller: Update to 1.28.0.•••* gnu/packages/bioinformatics.scm (r-biocinstaller): Update to 1.28.0. Ricardo Wurmus2017-11-07
* gnu: r-biocgenerics: Update to 0.24.0.•••* gnu/packages/bioinformatics.scm (r-biocgenerics): Update to 0.24.0. Ricardo Wurmus2017-11-07
* gnu: r-grohmm: Update to 1.12.0.•••* gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.12.0. Ricardo Wurmus2017-11-07
* gnu: r-shortread: Update to 1.36.0.•••* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.36.0. Ricardo Wurmus2017-11-07
* gnu: r-systempiper: Update to 1.12.0.•••* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.12.0. Ricardo Wurmus2017-11-07
* gnu: r-gseabase: Update to 1.40.0.•••* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.40.0. Ricardo Wurmus2017-11-07
* gnu: r-sva: Update to 3.26.0.•••* gnu/packages/bioinformatics.scm (r-sva): Update to 3.26.0. Ricardo Wurmus2017-11-07
* gnu: r-methylkit: Update to 1.4.0.•••* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.4.0. Ricardo Wurmus2017-11-07
* gnu: r-copywriter: Update to 2.10.0.•••* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.10.0. Ricardo Wurmus2017-11-07
* gnu: r-annotationfilter: Update to 1.2.0.•••* gnu/packages/bioinformatics.scm (r-annotationfilter): Update to 1.2.0. Ricardo Wurmus2017-11-07
* gnu: r-rhdf5: Update to 2.22.0.•••* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.22.0. Ricardo Wurmus2017-11-07
* gnu: r-tximport: Update to 1.6.0.•••* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.6.0. Ricardo Wurmus2017-11-07
* gnu: r-bamsignals: Update to 1.10.0.•••* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.10.0. Ricardo Wurmus2017-11-07
* gnu: r-zlibbioc: Update to 1.24.0.•••* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.24.0. Ricardo Wurmus2017-11-07
* gnu: r-rhtslib: Update to 1.10.0.•••* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.10.0. Ricardo Wurmus2017-11-07
* gnu: r-rbgl: Update to 1.54.0.•••* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.54.0. Ricardo Wurmus2017-11-07
* gnu: r-annotationforge: Update to 1.20.0.•••* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.20.0. Ricardo Wurmus2017-11-07
* gnu: r-dexseq: Update to 1.24.0.•••* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.0. Ricardo Wurmus2017-11-07
* gnu: r-deseq2: Update to 1.18.0.•••* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.18.0. Ricardo Wurmus2017-11-07
* gnu: r-genefilter: Update to 1.60.0.•••* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.60.0. Ricardo Wurmus2017-11-07
* gnu: r-geneplotter: Update to 1.56.0.•••* gnu/packages/bioinformatics.scm (r-geneplotter): Update to 1.56.0. Ricardo Wurmus2017-11-07
* gnu: r-annotate: Update to 1.56.0.•••* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.56.0. Ricardo Wurmus2017-11-07
* gnu: r-dnacopy: Update to 1.52.0.•••* gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.52.0. Ricardo Wurmus2017-11-07
* gnu: r-biocviews: Update to 1.46.0.•••* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.46.0. [propagated-inputs]: Remove r-knitr. Ricardo Wurmus2017-11-07
* gnu: r-bioccheck: Update to 1.14.0.•••* gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.14.0. [native-inputs]: Remove which. [propagated-inputs]: Add r-stringdist. Ricardo Wurmus2017-11-07
* gnu: diamond: Update to 0.9.12.•••* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.12. Ben Woodcroft2017-11-04
* gnu: multiqc: Update to 1.3.•••* gnu/packages/bioinformatics.scm (multiqc): Update to 1.3. [propagated-inputs]: Add python-enum34. [license]: The license was changed to "GPLv3 or later" with this release. Ricardo Wurmus2017-11-03
* gnu: r-ape: Update to 5.0.•••* gnu/packages/bioinformatics.scm (r-ape): Update to 5.0. [propagated-inputs]: Add r-rcpp. Ricardo Wurmus2017-11-03
* gnu: vsearch: Update to 2.5.2.•••* gnu/packages/bioinformatics.scm (vsearch): Update to 2.5.2. Ben Woodcroft2017-11-01
* gnu: diamond: Update to 0.9.11.•••* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.11. Ben Woodcroft2017-11-01
* gnu: Remove cufflinks.•••Cufflinks includes essential non-free code. Fixes <https://bugs.gnu.org/28946>. * gnu/packages/bioinformatics.scm (cufflinks): Remove variable. Ricardo Wurmus2017-10-31
* gnu: vsearch: Update to 2.5.1.•••* gnu/packages/bioinformatics.scm (vsearch): Update to 2.5.1. Ben Woodcroft2017-10-26
* gnu: bwa: Update to 0.7.17.•••* gnu/packages/bioinformatics.scm (bwa): Update to 0.7.17. Ben Woodcroft2017-10-25
* gnu: bwa: Change source URL to GitHub.•••* gnu/packages/bioinformatics.scm (bwa)[source]: Change source URL to GitHub. Ben Woodcroft2017-10-25
* gnu: miso: Update to 0.5.4.•••* gnu/packages/bioinformatics.scm (miso): Update to 0.5.4. Tobias Geerinckx-Rice2017-10-23
* Use HTTPS for bioconductor.org.•••* doc/guix.texi (Invoking guix import, Invoking guix refresh): Use HTTPS for bioconductor.org URLs. * gnu/packages/bioinformatics.scm (r-annotate, r-geneplotter, r-genefilter) (r-deseq2, r-dexseq, r-annotationforge, r-rbgl, r-gseabase, r-category) (r-gostats, r-shortread, r-biocgenerics, r-biocinstaller, r-biocviews) (r-biocstyle, r-bioccheck, r-s4vectors, r-iranges, r-genomeinfodbdata) (r-genomeinfodb, r-xvector, r-genomicranges, r-biobase, r-annotationdbi) (r-biomart, r-biocparallel, r-biostrings, r-rsamtools, r-delayedarray) (r-summarizedexperiment, r-genomicalignments, r-rtracklayer) (r-genomicfeatures, r-graph, r-topgo, r-bsgenome, r-impute, r-seqpattern) (r-seqlogo, r-motifrg, r-bamsignals, r-mutationalpatterns, r-tximport) (r-rhdf5, r-chipseq, r-sva, r-affy, r-vsn, r-mzid, r-msnid) (r-interactivedisplaybase, r-annotationhub)[home-page]: Likewise. * gnu/packages/bioinformatics.scm (r-txdb-hsapiens-ucsc-hg19-knowngene) (r-go-db, r-bsgenome-hsapiens-1000genomes-hs37d5, r-org-hs-eg-db) (r-org-ce-eg-db, r-org-dm-eg-db, r-org-mm-eg-db) (r-bsgenome-hsapiens-ucsc-hg19, r-bsgenome-mmusculus-ucsc-mm9) (r-bsgenome-mmusculus-ucsc-mm10, r-txdb-mmusculus-ucsc-mm10-knowngene) (r-bsgenome-celegans-ucsc-ce6, r-bsgenome-celegans-ucsc-ce10) (r-bsgenome-dmelanogaster-ucsc-dm3, r-copyhelper)[source, home-page]: Likewise. * gnu/packages/statistics.scm (r-rcurl)[source]: Likewise. * guix/build-system/r.scm (bioconductor-uri): Likewise. * guix/import/cran.scm (%cran-url, bioconductor-package?) (bioconductor-data-package?, bioconductor-experiment-package?): Likewise. Tobias Geerinckx-Rice2017-10-21
* gnu: f-seq: Fix location of commons-cli.jar.•••* gnu/packages/bioinformatics.scm (f-seq)[arguments]: Fix location of commons-cli.jar in the wrapper script. Ricardo Wurmus2017-10-18
* gnu: python-biopython: Update to 1.70.•••* gnu/packages/python.scm (python-biopython, python2-biopython): Update to 1.70. Cyril Roelandt2017-10-14
* gnu: Add plink-ng.•••* gnu/packages/bioinformatics.scm (plink-ng): New variable. Ricardo Wurmus2017-10-13
* gnu: Add paml.•••* gnu/packages/bioinformatics.scm (paml): New variable. Ricardo Wurmus2017-10-13
* gnu: clustal-omega: Update to 1.2.4.•••* gnu/packages/bioinformatics.scm (clustal-omega): Update to 1.2.4. Ricardo Wurmus2017-10-12
* gnu: f-seq: Truncate version string.•••* gnu/packages/bioinformatics.scm (f-seq)[version]: Truncate commit part of the version string. Ricardo Wurmus2017-10-12
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