diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 232 |
1 files changed, 229 insertions, 3 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index de37d19264..41cac296fe 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -617,6 +617,50 @@ Compared to cellSNP, this package is more efficient with higher speed and less memory usage.") (license license:asl2.0)))) +(define-public cpat + (package + (name "cpat") + (version "3.0.4") + (source (origin + (method url-fetch) + (uri (pypi-uri "CPAT" version)) + (sha256 + (base32 + "0dfrwwbhv1n4nh2a903d1qfb30fgxgya89sa70aci3wzf8h2z0vd")) + (modules '((guix build utils))) + (snippet + '(for-each delete-file-recursively + (list ".eggs" + "lib/__pycache__/" + "lib/cpmodule/__pycache__/"))))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (with-directory-excursion "test" + ;; There is no test4.fa + (substitute* "test.sh" + ((".*-g test4.fa.*") "")) + (invoke "bash" "test.sh")))))))) + (propagated-inputs + (list python-numpy python-pysam)) + (inputs + (list r-minimal)) + (home-page "https://wlcb.oit.uci.edu/cpat/") + (synopsis "Alignment-free distinction between coding and noncoding RNA") + (description + "CPAT is a method to distinguish coding and noncoding RNA by using a +logistic regression model based on four pure sequence-based, linguistic +features: ORF size, ORF coverage, Ficket TESTCODE, and Hexamer usage bias. +Linguistic features based method does not require other genomes or protein +databases to perform alignment and is more robust. Because it is +alignment-free, it runs much faster and also easier to use.") + (license license:gpl2+))) + (define-public pbcopper (package (name "pbcopper") @@ -1070,6 +1114,42 @@ of single-cell data using Seurat, RcppML nmf, SingleCellExperiments and similar.") (license license:gpl2+)))) +(define-public r-stacas + (package + (name "r-stacas") + (version "2.2.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/carmonalab/STACAS") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "13i0h5i6vlbrb8ndq9gr81560z9d74b2c7m3rjfzls01irjza9hm")))) + (properties `((upstream-name . "STACAS"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocneighbors + r-biocparallel + r-ggplot2 + r-ggridges + r-pbapply + r-r-utils + r-seurat)) + (home-page "https://github.com/carmonalab/STACAS") + (synopsis "Sub-type anchoring correction for alignment in Seurat") + (description + "This package implements methods for batch correction and integration of +scRNA-seq datasets, based on the Seurat anchor-based integration framework. +In particular, STACAS is optimized for the integration of heterogenous +datasets with only limited overlap between cell sub-types (e.g. TIL sets of +CD8 from tumor with CD8/CD4 T cells from lymphnode), for which the default +Seurat alignment methods would tend to over-correct biological differences. +The 2.0 version of the package allows the users to incorporate explicit +information about cell-types in order to assist the integration process.") + (license license:gpl3))) + (define-public r-stringendo (let ((commit "15594b1bba11048a812874bafec0eea1dcc8618a") (revision "1")) @@ -1156,6 +1236,32 @@ shape. This package provides an @code{htmlwidget} for building streamgraph visualizations.") (license license:expat)))) +(define-public r-wasabi + (let ((commit "8c33cabde8d18c2657cd6e38e7cb834f87cf9846") + (revision "1")) + (package + (name "r-wasabi") + (version (git-version "1.0.1" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/COMBINE-lab/wasabi") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0rpdj6n4cnx8n2zl60dzgl638474sg49dknwi9x3qb4g56dpphfa")))) + (properties `((upstream-name . "wasabi"))) + (build-system r-build-system) + (propagated-inputs (list r-data-table r-rhdf5 r-rjson)) + (home-page "https://github.com/COMBINE-lab/wasabi") + (synopsis "Use Sailfish and Salmon with Sleuth") + (description + "This package converts the output of the Sailfish and Salmon RNA-seq +quantification tools so that it can be used with the Sleuth differential +analysis package.") + (license license:bsd-3)))) + (define-public pbbam (package (name "pbbam") @@ -10313,6 +10419,51 @@ data. This package includes panel editing or renaming for FCS files, bead-based normalization and debarcoding.") (license license:gpl3)))) +(define-public r-projectils + (let ((commit "cc73b97471b4b6eea11ce779b5c4a7dc5c3e1709") + (revision "1")) + (package + (name "r-projectils") + (version (git-version "3.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/carmonalab/ProjecTILs") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0dpzvbhhb9andnj7angpj32cgkwd6rs6qgpl6i21pqzcn6vqqhqw")))) + (properties `((upstream-name . "ProjecTILs"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocneighbors + r-biocparallel + r-dplyr + r-ggplot2 + r-matrix + r-patchwork + r-pheatmap + r-pracma + r-purrr + r-rcolorbrewer + r-reshape2 + r-scales + r-scgate + r-seurat + r-seuratobject + r-stacas + r-ucell + r-umap + r-uwot)) + (home-page "https://github.com/carmonalab/ProjecTILs") + (synopsis "Reference-based analysis of scRNA-seq data") + (description + "This package implements methods to project single-cell RNA-seq data +onto a reference atlas, enabling interpretation of unknown cell transcriptomic +states in the the context of known, reference states.") + (license license:gpl3)))) + (define-public r-presto (let ((commit "052085db9c88aa70a28d11cc58ebc807999bf0ad") (revision "0")) @@ -10527,6 +10678,43 @@ analysis of cell types, subtypes, transcriptional gradients,cell-cycle variation, gene modules and their regulatory models and more.") (license license:expat)))) +(define-public r-sleuth + (package + (name "r-sleuth") + (version "0.30.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/pachterlab/sleuth") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "09xgc7r6iisjkk0c0wn0q56zy0aph386kphwixfzq4422y7vlqci")))) + (properties `((upstream-name . "sleuth"))) + (build-system r-build-system) + (propagated-inputs (list r-aggregation + r-data-table + r-dplyr + r-ggplot2 + r-lazyeval + r-matrixstats + r-pheatmap + r-reshape2 + r-rhdf5 + r-shiny + r-tidyr)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/pachterlab/sleuth") + (synopsis "Tools for investigating RNA-Seq") + (description + "Sleuth is a program for differential analysis of RNA-Seq data. +It makes use of quantification uncertainty estimates obtained via Kallisto for +accurate differential analysis of isoforms or genes, allows testing in the +context of experiments with complex designs, and supports interactive +exploratory data analysis via sleuth live.") + (license license:gpl3))) + (define-public r-snapatac (package (name "r-snapatac") @@ -17996,12 +18184,40 @@ The tool enables the de novo search for new structural elements and facilitates comparative analysis of known RNA families.") (license license:bsd-3))) +(define-public r-databaselinke-r + (let ((commit "cf3d6cc3d36f2e1c9a557390232e9a8ed5abb7fd") + (revision "1")) + (package + (name "r-databaselinke-r") + (version (git-version "1.7.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/vertesy/DatabaseLinke.R") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0hk76sb3w1v8a7c1knpc572ypsbgqlrv0p49c9y55a0dr12n16s1")))) + (properties `((upstream-name . "DatabaseLinke.R"))) + (build-system r-build-system) + (propagated-inputs (list r-readwriter)) + (home-page "https://github.com/vertesy/DatabaseLinke.R") + (synopsis + "Parse links to databases from your list of gene symbols") + (description + "This package provides a set of functions to parse and open (search +query) links to genomics related and other websites for R. Useful when you +want to explore e.g.: the function of a set of differentially expressed +genes.") + (license license:gpl3)))) + (define-public r-seurat-utils - (let ((commit "0b6f5b548a49148cfbeaa654e8a618c0a020afa5") + (let ((commit "c0374cc9e25ce391ba8013fda0f8c7babbb9201d") (revision "1")) (package (name "r-seurat-utils") - (version (git-version "1.6.5" revision commit)) + (version (git-version "2.5.0" revision commit)) (source (origin (method git-fetch) (uri (git-reference @@ -18010,12 +18226,15 @@ facilitates comparative analysis of known RNA families.") (file-name (git-file-name name version)) (sha256 (base32 - "1mn64h375mkj6x4ix5493z32gqg96yc507j5jr0lx9g5wk1bf762")))) + "15l86b43q245gzz7gsr5rhs4sir74lc14d64yqxfqcb0zrb2bzzd")))) (properties `((upstream-name . "Seurat.utils"))) (build-system r-build-system) (propagated-inputs (list r-codeandroll2 r-cowplot + r-databaselinke-r r-dplyr + r-enhancedvolcano + r-foreach r-ggcorrplot r-ggexpress r-ggplot2 @@ -18023,15 +18242,21 @@ facilitates comparative analysis of known RNA families.") r-ggrepel r-hgnchelper r-htmlwidgets + r-job + r-magrittr r-markdownhelpers r-markdownreports r-matrix r-matrixstats + r-pheatmap + r-plotly r-princurve + r-qs r-r-utils r-readr r-readwriter r-reshape2 + r-rstudioapi r-scales r-seurat r-soupx @@ -18040,6 +18265,7 @@ facilitates comparative analysis of known RNA families.") r-stringr r-tibble r-tictoc + r-tidyverse r-vroom)) (home-page "https://github.com/vertesy/Seurat.utils") (synopsis "Collection of utility functions for Seurat") |