progeny
This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see progeny.
Pathway RespOnsive GENes for activity inference from gene expression
Bioconductor version: 3.13
This package provides a function to infer pathway activity from gene expression using PROGENy. It contains the linear model we inferred in the publication "Perturbation-response genes reveal signaling footprints in cancer gene expression".
Author: Michael Schubert [aut], Alberto Valdeolivas [cre, ctb] 
, Christian H. Holland [ctb] , Igor Bulanov [ctb], Aurélien Dugourd [ctb]
Maintainer: Alberto Valdeolivas <alvaldeolivas at gmail.com>
citation("progeny")):
Installation
To install this package, start R (version "4.1") 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")| Applying PROGENy on single-cell RNA-seq data | HTML | R Script |
| PROGENy pathway signatures: Application to Bulk transcriptomics | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | FunctionalPrediction, GeneExpression, GeneRegulation, Software, SystemsBiology |
| Version | 1.14.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (6.5 years) |
| License | Apache License (== 2.0) | file LICENSE |
| Depends | R (>= 3.6.0) |
| Imports | Biobase, stats, dplyr, tidyr, ggplot2, ggrepel, gridExtra |
| 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, testthat (>= 2.1.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | mistyR |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | progeny_1.14.0.tar.gz |
| Windows Binary | progeny_1.14.0.zip |
| macOS 10.13 (High Sierra) | progeny_1.14.0.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 |
| Old Source Packages for BioC 3.13 | Source Archive |