progeny

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see progeny.

Pathway RespOnsive GENes for activity inference from gene expression


Bioconductor version: 3.7

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 <mschu.dev at gmail.com>

Maintainer: Michael Schubert <mschu.dev at gmail.com>

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

Installation

To install this package, start R (version "3.5") 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")
narray Usage Examples HTML R Script
Reference Manual PDF
LICENSE Text

Details

biocViews FunctionalPrediction, GeneExpression, GeneRegulation, Software, SystemsBiology
Version 1.2.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)
License Apache License (== 2.0) | file LICENSE
Depends R (>= 3.4.0)
Imports Biobase
System Requirements
URL https://github.com/saezlab/progeny
Bug Reports https://github.com/saezlab/progeny/issues
See More
Suggests airway, biomaRt, BiocFileCache, broom, DESeq2, dplyr, knitr, readr, readxl
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package progeny_1.2.0.tar.gz
Windows Binary progeny_1.2.0.zip
Mac OS X 10.11 (El Capitan) progeny_1.2.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/progeny
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/progeny
Package Short Url https://bioconductor.org/packages/progeny/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.7 Source Archive