progeny

This package is for version 3.6 of Bioconductor; for the stable, up-to-date release version, see progeny.

Pathway RespOnsive GENes for activity inference from gene expression

Bioconductor version: 3.6

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 "3.4") 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

Reference Manual PDF

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews FunctionalPrediction, GeneExpression, GeneRegulation, Software, SystemsBiology

Version 1.0.0

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

Suggests airway, biomaRt, BiocFileCache, broom, DESeq2, dplyr, knitr, readr, readxl

Linking To

Enhances

Depends On Me

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Package Archives

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

Source Package progeny_1.0.0.tar.gz

Windows Binary progeny_1.0.0.zip

Mac OS X 10.11 (El Capitan) progeny_1.0.0.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/

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Old Source Packages for BioC 3.6 Source Archive