GSEABase: Gene set enrichment data structures and methods

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This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA).

Author
Martin Morgan, Seth Falcon, Robert Gentleman
Date of publication
None
Maintainer
Bioconductor Package Maintainer <maintainer@bioconductor.org>
License
Artistic-2.0
Version
1.36.0

View on Bioconductor

Man pages

CollectionType-class
Class "CollectionType"
CollectionType-constructors
Collection Type Class Constructors
details-methods
Methods for Displaying Detailed GeneSet Information
GeneColorSet-class
Class "GeneColorSet"
GeneColorSet-methods
Methods to Construct "GeneColorSet" Instances
GeneIdentifierType-class
Class "GeneIdentifierType"
GeneIdentifierType-constructors
Gene Identifier Class Constructors
GeneSet-class
Class "GeneSet"
GeneSetCollection-class
Class "GeneSetCollection"
GeneSetCollection-methods
Methods to construct GeneSetCollection instances
GeneSet-methods
Methods to construct GeneSet instances
getObjects
Read and write gene sets from Broad or GMT formats
getOBOCollection
Read OBO-specified Gene Ontology Collections
goSlim-methods
Methods for Function goSlim in Package 'GSEABase'
GSEABase-package
Gene set enrichment data structures and methods
incidence-methods
Methods for Constructing Incidence Matricies Between GeneSets
mapIdentifiers-methods
Methods for Function mapIdentifiers in Package 'GSEABase'
OBOCollection-class
Class "OBOCollection"

Files in this package

GSEABase/DESCRIPTION
GSEABase/NAMESPACE
GSEABase/NEWS
GSEABase/R
GSEABase/R/AAA.R
GSEABase/R/AllClasses.R
GSEABase/R/AllGenerics.R
GSEABase/R/getObjects.R
GSEABase/R/methods-CollectionType.R
GSEABase/R/methods-ExpressionSet.R
GSEABase/R/methods-GeneColorSet.R
GSEABase/R/methods-GeneIdentifierType.R
GSEABase/R/methods-GeneSet.R
GSEABase/R/methods-GeneSetCollection.R
GSEABase/R/methods-OBOCollection.R
GSEABase/R/utilities.R
GSEABase/build
GSEABase/build/vignette.rds
GSEABase/inst
GSEABase/inst/doc
GSEABase/inst/doc/GSEABase.R
GSEABase/inst/doc/GSEABase.Rnw
GSEABase/inst/doc/GSEABase.pdf
GSEABase/inst/extdata
GSEABase/inst/extdata/Broad.xml
GSEABase/inst/extdata/Broad1.xml
GSEABase/inst/extdata/goslim_plant.obo
GSEABase/inst/unitTests
GSEABase/inst/unitTests/test_CollectionType.R
GSEABase/inst/unitTests/test_ExpressionSet.R
GSEABase/inst/unitTests/test_GeneColorSet.R
GSEABase/inst/unitTests/test_GeneIdentifierType.R
GSEABase/inst/unitTests/test_GeneSet.R
GSEABase/inst/unitTests/test_GeneSetCollection.R
GSEABase/inst/unitTests/test_OBOCollection.R
GSEABase/inst/unitTests/test_getGeneSets.R
GSEABase/inst/unitTests/test_utilities.R
GSEABase/man
GSEABase/man/CollectionType-class.Rd
GSEABase/man/CollectionType-constructors.Rd
GSEABase/man/GSEABase-package.Rd
GSEABase/man/GeneColorSet-class.Rd
GSEABase/man/GeneColorSet-methods.Rd
GSEABase/man/GeneIdentifierType-class.Rd
GSEABase/man/GeneIdentifierType-constructors.Rd
GSEABase/man/GeneSet-class.Rd
GSEABase/man/GeneSet-methods.Rd
GSEABase/man/GeneSetCollection-class.Rd
GSEABase/man/GeneSetCollection-methods.Rd
GSEABase/man/OBOCollection-class.Rd
GSEABase/man/details-methods.Rd
GSEABase/man/getOBOCollection.Rd
GSEABase/man/getObjects.Rd
GSEABase/man/goSlim-methods.Rd
GSEABase/man/incidence-methods.Rd
GSEABase/man/mapIdentifiers-methods.Rd
GSEABase/tests
GSEABase/tests/unitTests.R
GSEABase/vignettes
GSEABase/vignettes/GSEABase.Rnw