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.

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]
Date of publicationNone
MaintainerSoroor Hediyeh zadeh <hediyehzadeh.s@wehi.edu.au>
LicenseGPL-2
Version1.2.0

View on Bioconductor

Functions

bcm Man page
eset Man page
getSampleOutlier Man page
getSampleOutlier,matrix,nuchar-method Man page
getSampleOutlier,OPPARList,nuchar-method Man page
getSubtypeProbes Man page
getSubtypeProbes,matrix,nuchar-method Man page
getSubtypeProbes,OPPARList,nuchar-method Man page
gsva Man page
gsva,ExpressionSet,GeneSetCollection-method Man page
gsva,ExpressionSet,list-method Man page
gsva,matrix,GeneSetCollection-method Man page
gsva,matrix,list-method Man page
maupin Man page
opa Man page
opa,ExpressionSet-method Man page
opa,matrix-method Man page
oppar Man page
OPPARList-class Man page
$,OPPARList-method Man page
oppar-package Man page
show,OPPARList-method Man page

Files

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

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