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oppar

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

Outlier profile and pathway analysis in R


Bioconductor version: Development (3.19)

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>

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

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

Details

biocViews GeneExpression, GeneSetEnrichment, Pathways, Software, SystemsBiology
Version 1.31.0
In Bioconductor since BioC 3.3 (R-3.3) (8 years)
License GPL-2
Depends R (>= 3.3)
Imports Biobase, methods, GSEABase, GSVA
System Requirements
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Suggests knitr, rmarkdown, limma, org.Hs.eg.db, GO.db, snow, parallel
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Package Archives

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

Source Package oppar_1.31.0.tar.gz
Windows Binary oppar_1.31.0.zip
macOS Binary (x86_64) oppar_1.31.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/oppar
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/oppar
Bioc Package Browser https://code.bioconductor.org/browse/oppar/
Package Short Url https://bioconductor.org/packages/oppar/
Package Downloads Report Download Stats