progeny
This is the development version of progeny; for the stable release version, see progeny.
Pathway RespOnsive GENes for activity inference from gene expression
Bioconductor version: Development (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:
Maintainer: Aurélien Dugourd <aurelien.dugourd at bioquant.uni-heidelberg.de>
citation("progeny")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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")| PROGENy pathway signatures | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | FunctionalPrediction, GeneExpression, GeneRegulation, Software, SystemsBiology |
| Version | 1.29.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (7 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.
| Source Package | progeny_1.29.0.tar.gz |
| Windows Binary (x86_64) | progeny_1.29.0.zip (64-bit only) |
| macOS Binary (x86_64) | progeny_1.29.0.tgz |
| macOS Binary (arm64) | progeny_1.29.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/progeny |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/progeny |
| Bioc Package Browser | https://code.bioconductor.org/browse/progeny/ |
| Package Short Url | https://bioconductor.org/packages/progeny/ |
| Package Downloads Report | Download Stats |