To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("oppar")
In most cases, you don't need to download the package archive at all.
oppar
|
This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see oppar.
Outlier profile and pathway analysis in R
Bioconductor version: 3.3
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 and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("oppar")
Documentation
| HTML | R Script | OPPAR: Outlier Profile and Pathway Analysis in R |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | GeneExpression, GeneSetEnrichment, Pathways, Software, SystemsBiology |
| Version | 1.0.2 |
| In Bioconductor since | BioC 3.3 (R-3.3) (< 6 months) |
| 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 | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | oppar_1.0.2.tar.gz |
| Windows Binary | oppar_1.0.2.zip (32- & 64-bit) |
| Mac OS X 10.9 (Mavericks) | oppar_1.0.2.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/oppar/tree/release-3.3 |
| Package Short Url | http://bioconductor.org/packages/oppar/ |
| Package Downloads Report | Download Stats |
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