pathVar

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see pathVar.

Methods to Find Pathways with Significantly Different Variability

Bioconductor version: 3.16

This package contains the functions to find the pathways that have significantly different variability than a reference gene set. It also finds the categories from this pathway that are significant where each category is a cluster of genes. The genes are separated into clusters by their level of variability.

Author: Laurence de Torrente, Samuel Zimmerman, Jessica Mar

Maintainer: Samuel Zimmerman <samuel.e.zimmerman at gmail.com>

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

Installation

To install this package, start R (version "4.2") and enter:


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

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("pathVar")

Tutorial on How to Use the Functions in the \texttt{PathVar} Package PDF R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews GeneSetEnrichment, GeneticVariability, Pathways, Software

Version 1.28.0

In Bioconductor since BioC 3.2 (R-3.2) (8.5 years)

License LGPL (>= 2.0)

Depends R (>= 3.3.0), methods, ggplot2, gridExtra

Imports EMT, mclust, Matching, data.table, stats, grDevices, graphics, utils

System Requirements

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Package Archives

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

Source Package pathVar_1.28.0.tar.gz

Windows Binary pathVar_1.28.0.zip

macOS Binary (x86_64) pathVar_1.28.0.tgz

macOS Binary (arm64) pathVar_1.28.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/pathVar

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/pathVar

Bioc Package Browser https://code.bioconductor.org/browse/pathVar/

Package Short Url https://bioconductor.org/packages/pathVar/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.16 Source Archive