From 332177cd2d2da48d1a1f19671cb87e22adbf1f08 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 18 Oct 2021 12:28:55 +0200 Subject: gnu: Add r-seuratdisk. * gnu/packages/cran.scm (r-seuratdisk): New variable. --- gnu/packages/cran.scm | 43 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) (limited to 'gnu/packages/cran.scm') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 937f53784e..09023a4c79 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -28581,6 +28581,49 @@ algorithms; density clustering, hierarchical clustering, k-means, and the discovery of differentially expressed genes and markers.") (license license:gpl3))) +(define-public r-seuratdisk + (let ((commit "163f1aade5bac38ed1e9e9c912283a7e74781610") + (revision "1")) + (package + (name "r-seuratdisk") + (version (git-version "0.0.0.9019" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/mojaveazure/seurat-disk") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1d1v8qi6kknzy5fj6bl8akwy74h5h143i00lyidsnqjbwp9n4qnw")))) + (properties `((upstream-name . "SeuratDisk"))) + (build-system r-build-system) + (propagated-inputs + `(("r-cli" ,r-cli) + ("r-crayon" ,r-crayon) + ("r-hdf5r" ,r-hdf5r) + ("r-matrix" ,r-matrix) + ("r-r6" ,r-r6) + ("r-rlang" ,r-rlang) + ("r-seurat" ,r-seurat) + ("r-seuratobject" ,r-seuratobject) + ("r-stringi" ,r-stringi) + ("r-withr" ,r-withr))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/mojaveazure/seurat-disk") + (synopsis "Interfaces for HDF5-based single cell file formats") + (description + "The h5Seurat file format is specifically designed for the storage and +analysis of multi-modal single-cell and spatially-resolved expression +experiments, for example, from CITE-seq or 10X Visium technologies. It holds +all molecular information and associated metadata, including (for example) +nearest-neighbor graphs, dimensional reduction information, spatial +coordinates and image data, and cluster labels. This package also supports +rapid and on-disk conversion between h5Seurat and AnnData objects, with the +goal of enhancing interoperability between Seurat and Scanpy.") + (license license:gpl3)))) + (define-public r-phangorn (package (name "r-phangorn") -- cgit 1.4.1 From f51933aabcce43b837c06eda7add79df7b133850 Mon Sep 17 00:00:00 2001 From: Marcel Schilling Date: Wed, 20 Oct 2021 06:25:13 +0000 Subject: gnu: Add r-mhg. * gnu/packages/cran.scm (r-mhg): New variable. Signed-off-by: Ricardo Wurmus --- gnu/packages/cran.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) (limited to 'gnu/packages/cran.scm') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 09023a4c79..135baf6aa5 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -28879,6 +28879,26 @@ logging to plaintext, JSON, (rotating) files, memory buffers, and databases, as well as email and push notifications.") (license license:expat))) +(define-public r-mhg + (package + (name "r-mhg") + (version "1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "mHG" version)) + (sha256 + (base32 + "1rz5ncrvvv9h9grls15apa63v2nh9j87fmp4mwjjil37jx6a5zki")))) + (properties `((upstream-name . "mHG"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/package=mHG") + (synopsis "Minimum-hypergeometric test") + (description + "This package runs a minimum-hypergeometric (mHG) test as described in +\"Discovering Motifs in Ranked Lists of DNA Sequences\" by Eran Eden.") + (license license:gpl2))) + (define-public r-mlr3measures (package (name "r-mlr3measures") -- cgit 1.4.1 From c650160abb448d7de75e31dca3e35cd469bb8121 Mon Sep 17 00:00:00 2001 From: zimoun Date: Tue, 12 Oct 2021 22:46:50 +0200 Subject: gnu: Add r-pnwcolors. * gnu/packages/cran.scm (r-pnwcolors): New variable. --- gnu/packages/cran.scm | 23 ++++++++++++++++++++++- 1 file changed, 22 insertions(+), 1 deletion(-) (limited to 'gnu/packages/cran.scm') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 135baf6aa5..792ea2a75b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -31,7 +31,7 @@ ;;; Copyright © 2020 Antoine Côté ;;; Copyright © 2020 Arun Isaac ;;; Copyright © 2020 Magali Lemes -;;; Copyright © 2020 Simon Tournier +;;; Copyright © 2020, 2021 Simon Tournier ;;; Copyright © 2020 Aniket Patil ;;; Copyright © 2021 Marcel Schilling ;;; @@ -905,6 +905,27 @@ functions which can speed up workflow.") control over dimensions and appearance.") (license license:gpl2+))) +(define-public r-pnwcolors + (package + (name "r-pnwcolors") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "PNWColors" version)) + (sha256 + (base32 + "1phplnclkficfv8s6wsyrckk4ixzbayiy5iix6dddg40485l9nyj")))) + (properties `((upstream-name . "PNWColors"))) + (build-system r-build-system) + (home-page "https://github.com/jakelawlor/PNWColors") + (synopsis "Color palettes for data visualizations") + (description + "This package provides color palettes. They are checked for colorblind +accessibility from hue, saturation, and lightness value scaling using the +Chroma.js Color Palette Helper. See @url{https://gka.github.io/palettes}.") + (license license:cc0))) + (define-public r-ecp (package (name "r-ecp") -- cgit 1.4.1 From 2339ee166c73055604c9c3770b86f72b04b09ea8 Mon Sep 17 00:00:00 2001 From: jgart Date: Fri, 1 Oct 2021 05:26:06 -0400 Subject: gnu: Add r-fasterize. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/cran.scm (r-fasterize): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/cran.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) (limited to 'gnu/packages/cran.scm') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 792ea2a75b..d1f3e52b1e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -32117,6 +32117,34 @@ Python module, this utility provides a flexible and extensible way of formatting and delivering log messages with low overhead.") (license license:agpl3+))) +(define-public r-fasterize + (package + (name "r-fasterize") + (version "1.0.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "fasterize" version)) + (sha256 + (base32 "10bzl77c1b9jhcn1xp467qzp2n8c7s3wpxn53qjh1nwvbri5kd32")))) + (properties `((upstream-name . "fasterize"))) + (build-system r-build-system) + (propagated-inputs + `(("r-raster" ,r-raster) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-sp" ,r-sp))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/ecohealthalliance/fasterize") + (synopsis "Fast Polygon to Raster Conversion") + (description +"This package provides a drop-in replacement for @code{rasterize} from +the @code{raster} package that takes sf-type objects, and is much faster. +There is support for the main options provided by the @code{rasterize} +function, including setting the field used and background value, and +options for aggregating multi-layer rasters.") + (license license:expat))) + (define-public r-ggh4x (package (name "r-ggh4x") -- cgit 1.4.1 From f8d3c98162910b3d715c93f73ae9e7d278de6840 Mon Sep 17 00:00:00 2001 From: jgart Date: Fri, 1 Oct 2021 05:26:07 -0400 Subject: gnu: Add r-bien. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/cran.scm (r-bien): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/cran.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) (limited to 'gnu/packages/cran.scm') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index d1f3e52b1e..5448c52330 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -32145,6 +32145,43 @@ function, including setting the field used and background value, and options for aggregating multi-layer rasters.") (license license:expat))) +(define-public r-bien + (package + (name "r-bien") + (version "1.2.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "BIEN" version)) + (sha256 + (base32 "1dagrs54ciagm2mgqrvxl6k2akahr0qk63ifxqnks7iljm0x1gw6")))) + (properties `((upstream-name . "BIEN"))) + (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr) + ("r-testthat" ,r-testthat))) + (propagated-inputs + `(("r-ape" ,r-ape) + ("r-dbi" ,r-dbi) + ("r-doparallel" ,r-doparallel) + ("r-fasterize" ,r-fasterize) + ("r-foreach" ,r-foreach) + ("r-raster" ,r-raster) + ("r-rgdal" ,r-rgdal) + ("r-rgeos" ,r-rgeos) + ("r-rpostgresql" ,r-rpostgresql) + ("r-sf" ,r-sf) + ("r-sp" ,r-sp))) + (home-page "https://cran.r-project.org/package=BIEN") + (synopsis "Tools for accessing the BIEN database") + (description + "This package provides tools for accessing the Botanical Information and +Ecology Network (BIEN) database. The BIEN database contains cleaned and +standardized botanical data including occurrence, trait, plot and taxonomic +data. This package provides functions that query the BIEN database by +constructing and executing optimized SQL queries.") + (license license:expat))) + (define-public r-ggh4x (package (name "r-ggh4x") -- cgit 1.4.1 From cf0abb6cfe5222796b676fe2d1c7667fb396ce14 Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Thu, 28 Oct 2021 20:26:08 +0200 Subject: gnu: Add r-formattable. * gnu/packages/cran.scm (r-formattable): New variable. --- gnu/packages/cran.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) (limited to 'gnu/packages/cran.scm') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 5448c52330..5384dbcb29 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -23669,6 +23669,35 @@ univariate time series forecasts including exponential smoothing via state space models and automatic ARIMA modelling.") (license license:gpl3))) +(define-public r-formattable + (package + (name "r-formattable") + (version "0.2.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "formattable" version)) + (sha256 + (base32 "1vdxi0xmg019qyzjrp8bkjxciz245jcxsrkhfzd44ynqcwi4s3ag")))) + (properties `((upstream-name . "formattable"))) + (build-system r-build-system) + (propagated-inputs + `(("r-htmltools" ,r-htmltools) + ("r-htmlwidgets" ,r-htmlwidgets) + ("r-lifecycle" ,r-lifecycle) + ("r-rmarkdown" ,r-rmarkdown))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/renkun-ken/formattable") + (synopsis "Print vectors and data frames with text fromatting") + (description + "This R package provides functions to create formattable vectors and data +frames. @emph{Formattable} vectors are printed with text formatting, and +formattable data frames are printed with multiple types of formatting in HTML +to improve the readability of data presented in tabular form rendered in web +pages.") + (license license:expat))) + (define-public r-xmisc (package (name "r-xmisc") -- cgit 1.4.1