diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 121 |
1 files changed, 117 insertions, 4 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 508f5ea09a..3572f3d551 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1063,11 +1063,11 @@ plotnames, filenames and paths.") (license license:gpl3)))) (define-public r-readwriter - (let ((commit "71454f4aa706f5d2fbe606acd95abc14224e7058") + (let ((commit "12d32cb6533ef4b9eab4d707d1502525c2034aee") (revision "1")) (package (name "r-readwriter") - (version (git-version "0.2.9" revision commit)) + (version (git-version "0.3.2" revision commit)) (source (origin (method git-fetch) (uri (git-reference @@ -1076,7 +1076,7 @@ plotnames, filenames and paths.") (file-name (git-file-name name version)) (sha256 (base32 - "0sp27smhdva2hi2x0svia2l56k8xrh7p5akn78g5b0lcvz4x3hd7")))) + "1hy47g8d7zppr2i9zlkwl2yb0ii8x710hqk07h089ldx9171qxab")))) (properties `((upstream-name . "ReadWriter"))) (build-system r-build-system) (propagated-inputs @@ -5164,13 +5164,25 @@ software to answer ad hoc questions.") python-pysam python-pyyaml python-scipy + r-biocmanager + r-dplyr + r-genomicranges + r-here + r-openxlsx + r-optparse + r-readr + r-rsamtools + r-stringr + r-tidyr + r-upsetr + r-yaml snakemake-7)) (native-inputs (list python-cython python-pyfakefs python-pytest)) (home-page "https://github.com/dieterich-lab/Baltica") (synopsis "Integrated splice junction usage analysis") (description "This framework facilitates the execution of @dfn{differential junction -usage} (DJU) methods. Additionally, it enables the integration of results from +usage} (DJU) methods. Additionally, it enables the integration of results from multiple DJU methods.") (license license:expat))) @@ -10653,6 +10665,40 @@ of transcriptional heterogeneity among single cells.") ;; See https://github.com/hms-dbmi/scde/issues/38 (license license:gpl2))) +(define-public r-miamiplot + (let ((commit "beede9c5d6431b4d822aa42e064e01baeb5dd4a0") + (revision "1")) + (package + (name "r-miamiplot") + (version (git-version "1.1.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/juliedwhite/miamiplot") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0wxxk1lk9jbf0imf59qp302ffasvs84idinkvzirs3dw9w3589n9")))) + (properties `((upstream-name . "miamiplot"))) + (build-system r-build-system) + (propagated-inputs (list r-checkmate + r-dplyr + r-ggplot2 + r-ggrepel + r-gridextra + r-magrittr + r-rlang)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/juliedwhite/miamiplot") + (synopsis "Create a ggplot2 miami plot") + (description + "This package generates a Miami plot with centered chromosome labels. +The output is a ggplot2 object. Users can specify which data they want +plotted on top vs. bottom, whether to display significance line(s), what +colors to give chromosomes, and what points to label.") + (license license:gpl2)))) + (define-public r-millefy (package (name "r-millefy") @@ -18796,6 +18842,73 @@ transcriptional derivatives and visualization of the resulting velocity patterns.") (license license:gpl3)))) +(define-public r-voltron + (let ((commit "5057b703479239a9aaba761f07e65d849f6111f8") + (revision "1")) + (package + (name "r-voltron") + (version (git-version "1.0.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/BIMSBbioinfo/VoltRon") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1nximl4708a7fdwn8ysxpni3mp6dx33cphavlay7hh1pa55pnzgn")) + (modules '((guix build utils))) + ;; The tripack package is not available under a free license, + ;; but interp provides free implementations of "tri.mesh" and + ;; "neighbours". + (snippet + '(substitute* '("DESCRIPTION" "NAMESPACE" "R/spatial.R") + (("tripack") "interp"))))) + (properties `((upstream-name . "VoltRon"))) + (build-system r-build-system) + (inputs (list opencv tbb zlib)) + (propagated-inputs (list r-anndata + r-data-table + r-dplyr + r-ebimage + r-fastdummies + r-fnn + r-ggforce + r-ggplot2 + r-ggpubr + r-ggrepel + r-hdf5r + r-htmltools + r-igraph + r-interp + r-irlba + r-magick + r-matrix + r-morpho + r-raster + r-rcpp + r-reshape2 + r-rjson + r-rlang + r-s4vectors + r-scales + r-shiny + r-shinyjs + r-stringr + r-terra + r-umap + r-xml)) + (native-inputs (list pkg-config)) + (home-page "https://github.com/BIMSBbioinfo/VoltRon") + (synopsis "VoltRon for Spatial Data Integration and Analysis") + (description + "@code{VoltRon} is a toolbox for spatial data analysis, multi-omics +integration using spatial image registration. @code{VoltRon} is capable of +analyzing multiple types and modalities of spatially-aware datasets. +@code{VoltRon} visualizes and analyzes regions of interests (ROIs), spots, +cells and even molecules.") + (license license:expat)))) + (define-public methyldackel (package (name "methyldackel") |