oppar: Outlier profile and pathway analysis in R

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]
Date of publication
None
Maintainer
Soroor Hediyeh zadeh <hediyehzadeh.s@wehi.edu.au>
License
GPL-2
Version
1.2.0

View on Bioconductor

Man pages

bcm
Breast cancer metastases from different anatomical sites
eset
Tomlins et al. Prostate Cancer data (GEO: GSE6099)
getSampleOutlier
Retrieving outlier genes in samples
getSubtypeProbes
Retrieving outlier genes from a group of related samples
gsva
gsva
maupin
Maupin's TGFb data and a TGFb gene signature
opa
Outlier profile Analysis
oppar
oppar: A package for outlier profile and pathway analysis.
OPPARList-class
A S4 class for the output of OPPAR main function, opa.

Files in this package

oppar/DESCRIPTION
oppar/NAMESPACE
oppar/NEWS
oppar/R
oppar/R/class_OPPARList.R
oppar/R/class_nuchar.R
oppar/R/getSampleOutlier.R
oppar/R/getSubtypeProbes.R
oppar/R/gsva.R
oppar/R/opa-generic-methods.R
oppar/R/oppar.R
oppar/R/utils.R
oppar/R/zzz.R
oppar/build
oppar/build/vignette.rds
oppar/data
oppar/data/GSE46141.RData
oppar/data/Maupin.RData
oppar/data/datalist
oppar/data/tomlins.RData
oppar/inst
oppar/inst/CITATION
oppar/inst/doc
oppar/inst/doc/oppar.R
oppar/inst/doc/oppar.Rmd
oppar/inst/doc/oppar.html
oppar/man
oppar/man/OPPARList-class.Rd
oppar/man/bcm.Rd
oppar/man/eset.Rd
oppar/man/getSampleOutlier.Rd
oppar/man/getSubtypeProbes.Rd
oppar/man/gsva.Rd
oppar/man/maupin.Rd
oppar/man/opa.Rd
oppar/man/oppar.Rd
oppar/src
oppar/src/R_init_oppar.c
oppar/src/kernel_estimation.c
oppar/src/ks_test.c
oppar/src/matrix_density_R.h
oppar/vignettes
oppar/vignettes/oppar.Rmd