diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 113 |
1 files changed, 113 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 534204a16a..55d397e5cf 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -737,6 +737,44 @@ as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.") "This package exposes an annotation database generated from Ensembl.") (license license:artistic2.0))) +(define-public r-ensdb-hsapiens-v86 + (package + (name "r-ensdb-hsapiens-v86") + (version "2.99.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "EnsDb.Hsapiens.v86" version 'annotation)) + (sha256 + (base32 "1gp7xrzddpvmh2vrcp571wyy00skxgxfl39ksj4h0hm1qay0fb2m")))) + (properties `((upstream-name . "EnsDb.Hsapiens.v86"))) + (build-system r-build-system) + (propagated-inputs (list r-ensembldb)) + (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v86") + (synopsis "Ensembl based annotation package") + (description "This package exposes an annotation database generated from +Ensembl.") + (license license:artistic2.0))) + +(define-public r-ensdb-mmusculus-v79 + (package + (name "r-ensdb-mmusculus-v79") + (version "2.99.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "EnsDb.Mmusculus.v79" version 'annotation)) + (sha256 + (base32 "1zpmq7v55if6q9r0h883q9k8l70ym20b01m9hxf121wb256rl9f7")))) + (properties `((upstream-name . "EnsDb.Mmusculus.v79"))) + (build-system r-build-system) + (propagated-inputs (list r-ensembldb)) + (home-page "https://bioconductor.org/packages/EnsDb.Mmusculus.v79") + (synopsis "Ensembl based annotation package") + (description "This package exposes an annotation database generated from +Ensembl.") + (license license:artistic2.0))) + (define-public r-txdb-dmelanogaster-ucsc-dm6-ensgene (package (name "r-txdb-dmelanogaster-ucsc-dm6-ensgene") @@ -2966,6 +3004,44 @@ testing. The package also provides functions for the visualization and exploration of the results.") (license license:gpl3+))) +(define-public r-diffcyt + (package + (name "r-diffcyt") + (version "1.14.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "diffcyt" version)) + (sha256 + (base32 "1yc9mlc0ifb7h6rzskq97bsdq1kwdp5qq9l9mciwyxf6yjkmv5ni")))) + (properties `((upstream-name . "diffcyt"))) + (build-system r-build-system) + (propagated-inputs + (list r-circlize + r-complexheatmap + r-dplyr + r-edger + r-flowcore + r-flowsom + r-limma + r-lme4 + r-magrittr + r-multcomp + r-reshape2 + r-s4vectors + r-summarizedexperiment + r-tidyr)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/lmweber/diffcyt") + (synopsis "Differential discovery in high-dimensional cytometry") + (description + "This package provides statistical methods for differential discovery +analyses in high-dimensional cytometry data (including flow cytometry, mass +cytometry or CyTOF, and oligonucleotide-tagged cytometry), based on a +combination of high-resolution clustering and empirical Bayes moderated tests +adapted from transcriptomics.") + (license license:expat))) + (define-public r-dirichletmultinomial (package (name "r-dirichletmultinomial") @@ -4349,6 +4425,43 @@ differential expression analysis, RNAseq data and related problems.") ;; Any version of the LGPL (license license:lgpl3+))) +(define-public r-scannotatr + (package + (name "r-scannotatr") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "scAnnotatR" version)) + (sha256 + (base32 "08jq04ckjw8a5y753almc5bl8vnn4j6qp2zb7bb9w3ql3ddy7b21")))) + (properties `((upstream-name . "scAnnotatR"))) + (build-system r-build-system) + (propagated-inputs + (list r-annotationhub + r-ape + r-caret + r-data-tree + r-dplyr + r-e1071 + r-ggplot2 + r-kernlab + r-proc + r-rocr + r-seurat + r-singlecellexperiment + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/grisslab/scAnnotatR") + (synopsis "Pretrained models for prediction on single cell RNA-sequencing data") + (description + "This package comprises a set of pretrained machine learning models to +predict basic immune cell types. This enables to quickly get a first +annotation of the cell types present in the dataset without requiring prior +knowledge. The package also lets you train using own models to predict new +cell types based on specific research needs.") + (license license:expat))) + (define-public r-scdblfinder (package (name "r-scdblfinder") |