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pathVar

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This is the development version of pathVar; for the stable release version, see pathVar.

Methods to Find Pathways with Significantly Different Variability


Bioconductor version: Development (3.19)

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 "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("pathVar")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

Reference Manual PDF

Details

biocViews GeneSetEnrichment, GeneticVariability, Pathways, Software
Version 1.33.1
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
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Package Archives

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

Source Package
Windows Binary pathVar_1.33.1.zip
macOS Binary (x86_64) pathVar_1.33.1.tgz
macOS Binary (arm64) pathVar_1.33.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/pathVar
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/pathVar
Package Short Url https://bioconductor.org/packages/pathVar/
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