diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 44 |
1 files changed, 28 insertions, 16 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4320bc0bb5..28522e7c13 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2649,6 +2649,8 @@ interactive exploration of results.") ("r-singlecellexperiment" ,r-singlecellexperiment) ("r-stringr" ,r-stringr) ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/RGLab/MAST/") (synopsis "Model-based analysis of single cell transcriptomics") (description @@ -3393,20 +3395,22 @@ information about samples and features can be added to the plot.") (define-public r-gosemsim (package (name "r-gosemsim") - (version "2.12.0") + (version "2.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GOSemSim" version)) (sha256 (base32 - "0pqnlgdvh5szjhwc1mw1snjgpj9lrsnk44bn164cl3zwvdayccya")))) + "1r8yx6qw6d6602cp8aspzl3shi1l1zqcrc8fm9d5wg01sw1whs05")))) (properties `((upstream-name . "GOSemSim"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-go-db" ,r-go-db) ("r-rcpp" ,r-rcpp))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://guangchuangyu.github.io/software/GOSemSim") (synopsis "GO-terms semantic similarity measures") (description @@ -5316,14 +5320,14 @@ coefficients).") (define-public r-biosigner (package (name "r-biosigner") - (version "1.14.0") + (version "1.14.4") (source (origin (method url-fetch) (uri (bioconductor-uri "biosigner" version)) (sha256 (base32 - "1kdfhw629qczrfms0jmphqz0ksjzi8js00xj92h1lnv092npfk0j")))) + "0hypk784xcax99mp673md6kvx45chk2nxbqniww7zm9q2hj983hl")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -5332,10 +5336,7 @@ coefficients).") ("r-randomforest" ,r-randomforest) ("r-ropls" ,r-ropls))) (native-inputs - `(("r-knitr" ,r-knitr) - ("r-rmarkdown" ,r-rmarkdown) - ("pandoc" ,ghc-pandoc) - ("pandoc-citeproc" ,ghc-pandoc-citeproc))) ; all for vignettes + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/biosigner/") (synopsis "Signature discovery from omics data") (description @@ -6630,7 +6631,8 @@ measures.") ("r-gplots" ,r-gplots) ("r-limma" ,r-limma) ("r-rcolorbrewer" ,r-rcolorbrewer))) - (home-page "http://www.ebi.ac.uk/bertone/software") + (home-page (string-append "https://www.ebi.ac.uk/sites/ebi.ac.uk/files/" + "groups/bertone/software/HTqPCR.pdf")) (synopsis "Automated analysis of high-throughput qPCR data") (description "Analysis of Ct values from high throughput quantitative real-time @@ -6997,14 +6999,14 @@ a file-backed matrix with factor properties.") (define-public r-bigpint (package (name "r-bigpint") - (version "1.2.0") + (version "1.2.2") (source (origin (method url-fetch) (uri (bioconductor-uri "bigPint" version)) (sha256 (base32 - "10vs0lzfyxp6sm4r9pxfwipjvzmmaqnvwn1hc5q37s5qz44fg0hk")))) + "1zkakxi1iqavzmjxnkkd02qm5jk28ldcvcdcxaafz748dz6s67fs")))) (properties `((upstream-name . "bigPint"))) (build-system r-build-system) (propagated-inputs @@ -7024,6 +7026,8 @@ a file-backed matrix with factor properties.") ("r-shinydashboard" ,r-shinydashboard) ("r-stringr" ,r-stringr) ("r-tidyr" ,r-tidyr))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/lindsayrutter/bigPint") (synopsis "Big multivariate data plotted interactively") (description @@ -7298,14 +7302,14 @@ access.") (define-public r-multiassayexperiment (package (name "r-multiassayexperiment") - (version "1.12.4") + (version "1.12.6") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiAssayExperiment" version)) (sha256 (base32 - "01cnp00y5bk551c8gqgqp5468dvccg72i0rvh5cxgbx1c42zy6xn")))) + "174vzlxsyayb5il77cb3zzgszxl3l0wkprc9w6pgz4yv5ix13adi")))) (properties `((upstream-name . "MultiAssayExperiment"))) (build-system r-build-system) @@ -7317,6 +7321,8 @@ access.") ("r-s4vectors" ,r-s4vectors) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-tidyr" ,r-tidyr))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://waldronlab.io/MultiAssayExperiment/") (synopsis "Integration of multi-omics experiments in Bioconductor") (description @@ -7401,18 +7407,19 @@ gene selection, testing relationships, and so on.") (define-public r-biocpkgtools (package (name "r-biocpkgtools") - (version "1.4.0") + (version "1.4.6") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocPkgTools" version)) (sha256 (base32 - "0gyhb3071pxmvaxla7cxy9k97s3z3ynl62jnqz9jnkd53c7jnd53")))) + "0grwnmncmpqcplbfw3j210m1a8f7mmdizklh4zksg4ic21dpjj1a")))) (properties `((upstream-name . "BiocPkgTools"))) (build-system r-build-system) (propagated-inputs - `(("r-biocmanager" ,r-biocmanager) + `(("r-biocfilecache" ,r-biocfilecache) + ("r-biocmanager" ,r-biocmanager) ("r-biocviews" ,r-biocviews) ("r-dplyr" ,r-dplyr) ("r-dt" ,r-dt) @@ -7424,14 +7431,19 @@ gene selection, testing relationships, and so on.") ("r-igraph" ,r-igraph) ("r-jsonlite" ,r-jsonlite) ("r-magrittr" ,r-magrittr) + ("r-rappdirs" ,r-rappdirs) ("r-rbgl" ,r-rbgl) ("r-readr" ,r-readr) ("r-rex" ,r-rex) + ("r-rlang" ,r-rlang) ("r-rvest" ,r-rvest) ("r-stringr" ,r-stringr) ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr) + ("r-tidyselect" ,r-tidyselect) ("r-xml2" ,r-xml2))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/seandavi/BiocPkgTools") (synopsis "Collection of tools for learning about Bioconductor packages") (description |