EGSEA: Ensemble of Gene Set Enrichment Analyses

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This package implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing.

Author
Monther Alhamdoosh, Milica Ng and Matthew Ritchie
Date of publication
None
Maintainer
Monther Alhamdoosh <m.hamdoosh@gmail.com>
License
GPL-2
Version
1.2.0

View on Bioconductor

Man pages

buildCustomIdx
Custom Gene Set Collection Index
buildGeneSetDBIdx
Gene Set Collection Indexes from the GeneSetDB Database
buildIdx
Generate Gene Set Collection Indexes from the MSigDB and KEGG...
buildKEGGIdx
Gene Set Collection Index from the KEGG Database
buildMSigDBIdx
Gene Set Collection Indexes from the MSigDB Database
egsea
Ensemble of Gene Set Enrichment Analyses Function
egsea.base
EGSEA Base GSE Methods
egsea.cnt
Ensemble of Gene Set Enrichment Analyses Function
egsea.combine
EGSEA P-value Combining Options
egsea.ora
Over-representation Analysis with EGSEA Reporting...
EGSEA-package
Ensemble of Gene Enrichment Analysis (EGSEA)
EGSEAResults-methods
The EGSEAResults class
egsea.sort
EGSEA Result Sorting Options
GSCollectionIndex-methods
The GSCollectionIndex class

Files in this package

EGSEA/DESCRIPTION
EGSEA/NAMESPACE
EGSEA/NEWS
EGSEA/R
EGSEA/R/EGSEAclass.R
EGSEA/R/GSCollectionIndexclass.R
EGSEA/R/egsea.R
EGSEA/R/egseaUtils.R
EGSEA/R/fisher.method.R
EGSEA/R/gsacamera.R
EGSEA/R/gsafry.R
EGSEA/R/gsagage.R
EGSEA/R/gsaglobaltest.R
EGSEA/R/gsagsva.R
EGSEA/R/gsaora.R
EGSEA/R/gsapadog.R
EGSEA/R/gsaplots.R
EGSEA/R/gsaroast.R
EGSEA/R/gsasafe.R
EGSEA/R/htmlUtils.R
EGSEA/R/idxAnno.R
EGSEA/README.md
EGSEA/build
EGSEA/build/vignette.rds
EGSEA/inst
EGSEA/inst/doc
EGSEA/inst/doc/EGSEA.R
EGSEA/inst/doc/EGSEA.Rnw
EGSEA/inst/doc/EGSEA.pdf
EGSEA/man
EGSEA/man/EGSEA-package.Rd
EGSEA/man/EGSEAResults-methods.Rd
EGSEA/man/GSCollectionIndex-methods.Rd
EGSEA/man/buildCustomIdx.Rd
EGSEA/man/buildGeneSetDBIdx.Rd
EGSEA/man/buildIdx.Rd
EGSEA/man/buildKEGGIdx.Rd
EGSEA/man/buildMSigDBIdx.Rd
EGSEA/man/egsea.Rd
EGSEA/man/egsea.base.Rd
EGSEA/man/egsea.cnt.Rd
EGSEA/man/egsea.combine.Rd
EGSEA/man/egsea.ora.Rd
EGSEA/man/egsea.sort.Rd
EGSEA/tests
EGSEA/tests/testthat
EGSEA/tests/testthat.R
EGSEA/tests/testthat/test_EGSEA.R
EGSEA/vignettes
EGSEA/vignettes/EGSEA.Rnw
EGSEA/vignettes/egsea_classes-crop.pdf
EGSEA/vignettes/egsea_report-crop.pdf
EGSEA/vignettes/egsea_results-crop.pdf
EGSEA/vignettes/references.bib