progeny
Pathway RespOnsive GENes for activity inference from gene expression
Bioconductor version: 3.24 · Package version: 1.35.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
PROGENy is resource that leverages a large compendium of publicly available signaling perturbation experiments to yield a common core of pathway responsive genes for human and mouse. These, coupled with any statistical method, can be used to infer pathway activities from bulk or single-cell transcriptomics.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("progeny")Details
| Maintainer | Aurélien Dugourd <aurelien.dugourd@bioquant.uni-heidelberg.de> |
| Author | Michael Schubert [aut], Alberto Valdeolivas [ctb] (ORCID: <https://orcid.org/0000-0001-5482-9023>), Christian H. Holland [ctb] (ORCID: <https://orcid.org/0000-0002-3060-5786>), Igor Bulanov [ctb], Aurélien Dugourd [cre, ctb] |
| License | Apache License (== 2.0) | file LICENSE |
| URL | https://github.com/saezlab/progeny |
| Bug Reports | https://github.com/saezlab/progeny/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | FunctionalPrediction, GeneExpression, GeneRegulation, Software, SystemsBiology |
| Package Short Url | https://bioconductor.org/packages/progeny/ |
Citation
From within R, enter citation("progeny"):
Michael Schubert. progeny: Pathway RespOnsive GENes for activity inference from gene expression. doi:10.18129/B9.bioc.progeny, R package version 1.35.0, https://bioconductor.org/packages/progeny.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Dependencies
Depends: R (>= 3.6.0)
Imports: Biobase, stats, dplyr, tidyr, ggplot2, ggrepel, gridExtra, decoupleR, reshape2
Suggests: airway, biomaRt, BiocFileCache, broom, Seurat, SingleCellExperiment, DESeq2, BiocStyle, knitr, readr, readxl, pheatmap, tibble, rmarkdown, testthat (>= 2.1.0)
Reverse dependencies
Suggests Me (1): autonomics