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 (3.24)
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("oppar")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text |
Details
| biocViews | GeneExpression, GeneSetEnrichment, Pathways, Software, SystemsBiology |
| Version | 1.41.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (10.5 years) |
| License | GPL-2 |
| Depends | R (>= 3.3) |
| Imports | Biobase, methods, GSEABase, GSVA |
| System Requirements | |
| URL |
See More
| Suggests | knitr, rmarkdown, limma, org.Hs.eg.db, GO.db, snow, parallel |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | oppar_1.41.0.tar.gz |
| Windows Binary (x86_64) | oppar_1.41.0.zip |
| macOS Binary (big-sur-x86_64) | oppar_1.41.0.tgz |
| macOS Binary (sonoma-arm64) | oppar_1.41.0.tgz |
| 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 |