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Bioconductor - progeny

progeny

This is the released version of progeny; for the devel version, see progeny.

Pathway RespOnsive GENes for activity inference from gene expression

Bioconductor version: Release (3.21)

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.

Author: Michael Schubert [aut], Alberto Valdeolivas [ctb] ORCID: 0000-0001-5482-9023 , Christian H. Holland [ctb] ORCID: 0000-0002-3060-5786 , Igor Bulanov [ctb], Aurélien Dugourd [cre, ctb]

Maintainer: Aurélien Dugourd <aurelien.dugourd at bioquant.uni-heidelberg.de>

Citation (from within R, enter citation("progeny")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("progeny")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("progeny")
Details biocViews FunctionalPrediction, GeneExpression, GeneRegulation, Software, SystemsBiology Version 1.30.0 In Bioconductor since BioC 3.6 (R-3.4) (7.5 years) License Apache License (== 2.0) | file LICENSE Depends R (>= 3.6.0) Imports Biobase, stats, dplyr, tidyr, ggplot2, ggrepel, gridExtra, decoupleR, reshape2 System Requirements URL https://github.com/saezlab/progeny Bug Reports https://github.com/saezlab/progeny/issues See More Suggests airway, biomaRt, BiocFileCache, broom, Seurat, SingleCellExperiment, DESeq2, BiocStyle, knitr, readr, readxl, pheatmap, tibble, rmarkdown, testthat (>= 2.1.0) Linking To Enhances Depends On Me Imports Me easier Suggests Me autonomics Links To Me Build Report Build Report Package Archives

Follow Installation instructions to use this package in your R session.

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