oppar

DOI: 10.18129/B9.bioc.oppar    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see oppar.

Outlier profile and pathway analysis in R

Bioconductor version: 3.12

The R implementation of mCOPA package published by Wang et al. (2012). Oppar provides methods for Cancer Outlier profile Analysis. Although initially developed to detect outlier genes in cancer studies, methods presented in oppar can be used for outlier profile analysis in general. In addition, tools are provided for gene set enrichment and pathway analysis.

Author: Chenwei Wang [aut], Alperen Taciroglu [aut], Stefan R Maetschke [aut], Colleen C Nelson [aut], Mark Ragan [aut], Melissa Davis [aut], Soroor Hediyeh zadeh [cre], Momeneh Foroutan [ctr]

Maintainer: Soroor Hediyeh zadeh <hediyehzadeh.s at wehi.edu.au>

Installation

To install this package, start R (version "4.0") and enter:

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

BiocManager::install("oppar")

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("oppar")

 

HTML	R Script	OPPAR: Outlier Profile and Pathway Analysis in R
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneExpression, GeneSetEnrichment, Pathways, Software, SystemsBiology
Version	1.18.0
In Bioconductor since	BioC 3.3 (R-3.3) (5 years)
License	GPL-2
Depends	R (>= 3.3)
Imports	Biobase, methods, GSEABase, GSVA
LinkingTo
Suggests	knitr, rmarkdown, limma, org.Hs.eg.db, GO.db, snow, parallel
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	oppar_1.18.0.tar.gz
Windows Binary	oppar_1.18.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	oppar_1.18.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/oppar
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/oppar
Package Short Url	https://bioconductor.org/packages/oppar/
Package Downloads Report	Download Stats