diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 170 |
1 files changed, 170 insertions, 0 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 7fa47aee1c..0a502a6063 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -72,6 +72,7 @@ #:use-module (gnu packages mpi) #:use-module (gnu packages multiprecision) #:use-module (gnu packages networking) + #:use-module (gnu packages node) #:use-module (gnu packages pcre) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) @@ -103,6 +104,76 @@ The package provides functions for point generation, arc length estimation, degree elevation and curve fitting.") (license license:gpl2+))) +(define-public r-v8 + (package + (name "r-v8") + (version "3.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "V8" version)) + (sha256 + (base32 + "0xdljralgwyivdhx2a7kqf3yv4ijl4rdrz2p7p59lj2x5d2qyanf")))) + (properties `((upstream-name . "V8"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'find-v8 + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "configure" + (("^PKG_LIBS=.*") + (string-append "PKG_LIBS=" + (assoc-ref inputs "node") + "/lib/libnode.so.64\n"))) + (setenv "INCLUDE_DIR" + (string-append + (assoc-ref inputs "node") + "/include/node")) + (setenv "LIB_DIR" + (string-append + (assoc-ref inputs "node") "/lib")) + #t))))) + (inputs + `(("node" ,libnode))) + (propagated-inputs + `(("r-curl" ,r-curl) + ("r-jsonlite" ,r-jsonlite) + ("r-rcpp" ,r-rcpp))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://jeroen.cran.dev/V8") + (synopsis "Embedded JavaScript and WebAssembly engine for R") + (description + "This package provides an R interface to V8: Google's JavaScript and +WebAssembly engine.") + (license license:expat))) + +(define-public r-dot + (package + (name "r-dot") + (version "0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "DOT" version)) + (sha256 + (base32 + "0qh5n57cp9c2n5yn59q4wggz82943pwfanp3kx869aba2x3sj30i")))) + (properties `((upstream-name . "DOT"))) + (build-system r-build-system) + (propagated-inputs + `(("r-v8" ,r-v8))) + (home-page "http://haghish.com/dot") + (synopsis "Render and Export DOT Graphs in R") + (description + "This package provides tools to render DOT diagram markup language in R +and also provides the possibility to export the graphs in PostScript and +SVG (Scalable Vector Graphics) formats. In addition, it supports literate +programming packages such as @code{knitr} and @code{rmarkdown}.") + (license license:expat))) + (define-public r-clipr (package (name "r-clipr") @@ -158,6 +229,77 @@ the system clipboards.") respecting the grammar of its graphics paradigm.") (license license:gpl2+))) +(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-gprofiler2 + (package + (name "r-gprofiler2") + (version "0.1.9") + (source + (origin + (method url-fetch) + (uri (cran-uri "gprofiler2" version)) + (sha256 + (base32 + "112hmmvdwg8xz90w1bsbzc55y4xi9jj4dqy0q4bsgp49x58r92rb")))) + (properties `((upstream-name . "gprofiler2"))) + (build-system r-build-system) + (propagated-inputs + `(("r-crosstalk" ,r-crosstalk) + ("r-dplyr" ,r-dplyr) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-jsonlite" ,r-jsonlite) + ("r-plotly" ,r-plotly) + ("r-rcurl" ,r-rcurl) + ("r-tidyr" ,r-tidyr) + ("r-viridislite" ,r-viridislite))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://cran.r-project.org/web/packages/gprofiler2/") + (synopsis "Interface to the g:Profiler toolset") + (description + "This package provides a toolset for functional enrichment analysis and +visualization, gene/protein/SNP identifier conversion and mapping orthologous +genes across species via @url{https://biit.cs.ut.ee/gprofiler,g:Profiler}. +The main tools are: + +@enumerate +@item @code{g:GOSt}, functional enrichment analysis and visualization of gene + lists; +@item @code{g:Convert}, gene/protein/transcript identifier conversion across + various namespaces; +@item @code{g:Orth}, orthology search across species; +@item @code{g:SNPense}, mapping SNP rs identifiers to chromosome positions, + genes and variant effects. +@end enumerate + +This package is an R interface corresponding to the 2019 update of +@code{g:Profiler} and provides access to versions @code{e94_eg41_p11} and +higher.") + (license license:gpl2+))) + (define-public r-oenb (package (name "r-oenb") @@ -21853,3 +21995,31 @@ with posterior predictive checks and leave-one-out cross-validation.") and prediction with Aalen-Johansen or simulation in competing risks and multi-state models.") (license license:gpl2+))) + +(define-public r-scatterpie + (package + (name "r-scatterpie") + (version "0.1.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "scatterpie" version)) + (sha256 + (base32 + "0g5sn0iv6c1q7y51j4gbbbnil5089dgk1w4q94c7h5y3x7wfrzqb")))) + (properties `((upstream-name . "scatterpie"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggforce" ,r-ggforce) + ("r-ggplot2" ,r-ggplot2) + ("r-rlang" ,r-rlang) + ("r-rvcheck" ,r-rvcheck) + ("r-tidyr" ,r-tidyr))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://cran.r-project.org/web/packages/scatterpie/") + (synopsis "Scatter pie plot") + (description + "This package creates scatterpie plots, especially useful for plotting +pies on a map.") + (license license:artistic2.0))) |