oppar: Outlier profile and pathway analysis in R
Version 1.4.0

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.

AuthorChenwei 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]
Bioconductor views GeneExpression GeneSetEnrichment Pathways Software SystemsBiology
Date of publicationNone
MaintainerSoroor Hediyeh zadeh <hediyehzadeh.s@wehi.edu.au>
LicenseGPL-2
Version1.4.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("oppar")

Getting started

OPPAR: Outlier Profile and Pathway Analysis in R

Popular man pages

eset: Tomlins et al. Prostate Cancer data (GEO: GSE6099)
getSampleOutlier: Retrieving outlier genes in 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.
See all...

All man pages Function index File listing

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.

Functions

$,OPPARList-method Man page
OPPARList-class Man page
bcm Man page
combinez Source code
compute.gene.density Source code
compute.geneset.es Source code
compute.gset.overlap.score Source code
compute.null.enrichment Source code
computeGeneSetsOverlap Source code
eset Man page
getOutlier Source code
getSampleOutlier Man page
getSampleOutlier,OPPARList,nuchar-method Man page
getSampleOutlier,matrix,nuchar-method Man page
getSubtypeProbes Man page
getSubtypeProbes,OPPARList,nuchar-method Man page
getSubtypeProbes,matrix,nuchar-method Man page
get_q Source code
gsva Man page Source code
gsva,ExpressionSet,GeneSetCollection-method Man page
gsva,ExpressionSet,list-method Man page
gsva,matrix,GeneSetCollection-method Man page
gsva,matrix,list-method Man page
ks_test_Rcode Source code
ks_test_m Source code
load.gmt.data Source code
maupin Man page
onLoad Source code
opa Man page
opa,ExpressionSet-method Man page
opa,matrix-method Man page
oppar Man page
oppar-package Man page
plage Source code
rightsingularsvdvectorgset Source code
rndWalk Source code
sPackageLoaded Source code
show,OPPARList-method Man page
ssgsea Source code
zscore Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/class_OPPARList.R
R/class_nuchar.R
R/getSampleOutlier.R
R/getSubtypeProbes.R
R/gsva.R
R/opa-generic-methods.R
R/oppar.R
R/utils.R
R/zzz.R
build
build/vignette.rds
data
data/GSE46141.RData
data/Maupin.RData
data/datalist
data/tomlins.RData
inst
inst/CITATION
inst/doc
inst/doc/oppar.R
inst/doc/oppar.Rmd
inst/doc/oppar.html
man
man/OPPARList-class.Rd
man/bcm.Rd
man/eset.Rd
man/getSampleOutlier.Rd
man/getSubtypeProbes.Rd
man/gsva.Rd
man/maupin.Rd
man/opa.Rd
man/oppar.Rd
src
src/R_init_oppar.c
src/kernel_estimation.c
src/ks_test.c
src/matrix_density_R.h
vignettes
vignettes/oppar.Rmd
oppar documentation built on May 20, 2017, 9:40 p.m.

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