Package: GSEABase 1.69.0

Bioconductor Package Maintainer

GSEABase: Gene set enrichment data structures and methods

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

Authors:Martin Morgan [aut], Seth Falcon [aut], Robert Gentleman [aut], Paul Villafuerte [ctb], Bioconductor Package Maintainer [cre]

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NEWS

# Install 'GSEABase' in R:

install.packages('GSEABase', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:GSEABase-1.67.1(bioc 3.20)GSEABase-1.66.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

geneexpression genesetenrichment graphandnetwork go kegg

10.27 score 80 packages 1.5k scripts 13k downloads 79 mentions 88 exports 42 dependencies

Last updated 22 days agofrom:9f00f81bb1. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win	OK	Oct 31 2024
R-4.5-linux	OK	Oct 30 2024
R-4.4-win	OK	Oct 31 2024
R-4.4-mac	OK	Oct 31 2024
R-4.3-win	OK	Oct 31 2024
R-4.3-mac	OK	Oct 31 2024

Exports:AnnoOrEntrezIdentifier annotation annotation<-AnnotationIdentifier asBroadUri bcCategory bcSubCategory BroadCollection ChrCollection ChrlocCollection coerce collectionType collectionType<-coloring coloring<-ComputedCollection contributor contributor<-creationDate creationDate<-description description<-details ENSEMBLIdentifier EntrezIdentifier EnzymeIdentifier evidenceCode ExpressionSetCollection geneColor geneColor<-GeneColorSet geneIds geneIds<-geneIdType geneIdType<-GenenameIdentifier GeneSet GeneSetCollection getBroadSets getGmt getOBOCollection GOAllFrameIdentifier GOCollection goSlim ids incidence initialize intersect KEGGCollection Logic longDescription longDescription<-MapCollection mapIdentifiers NullCollection NullIdentifier OBOCollection OMIMCollection ontology organism organism<-PfamCollection phenotype phenotype<-phenotypeColor phenotypeColor<-PMIDCollection PrositeCollection pubMedIds pubMedIds<-RefseqIdentifier setdiff setIdentifier setIdentifier<-setName setName<-setVersion setVersion<-show subsets SymbolIdentifier toBroadXML toGmt union UniprotIdentifier updateObject urls urls<-

Dependencies:annotate AnnotationDbi askpass Biobase BiocGenerics Biostrings bit bit64 blob cachem cli cpp11 crayon curl DBI fastmap GenomeInfoDb GenomeInfoDbData glue graph httr IRanges jsonlite KEGGREST lifecycle memoise mime openssl pkgconfig plogr png R6 rlang RSQLite S4Vectors sys UCSC.utils vctrs XML xtable XVector zlibbioc

An introduction to GSEABase

Martin Morgan, Paul Villafuerte

Rendered fromGSEABase.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2023-02-24
Started: 2023-02-24

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Gene set enrichment data structures and methods	GSEABase-package GSEABase
Collection Type Class Constructors	BroadCollection ChrCollection ChrlocCollection CollectionType ComputedCollection ExpressionSetCollection GOCollection KEGGCollection MapCollection NullCollection OBOCollection OMIMCollection PfamCollection PMIDCollection PrositeCollection
Class "CollectionType"	&,CollectionIdType,CollectionIdType-method &,CollectionType,CollectionType-method bcCategory bcCategory,BroadCollection-method bcSubCategory bcSubCategory,BroadCollection-method BroadCollection-class ChrCollection-class ChrlocCollection-class CollectionIdType-class collectionType,CollectionType-method CollectionType-class ComputedCollection-class evidenceCode evidenceCode,GOCollection-method ExpressionSetCollection-class GOCollection-class goIds goIds,GOCollection-method ids ids,CollectionIdType-method intersect,CollectionIdType,CollectionIdType-method intersect,CollectionType,CollectionType-method KEGGCollection-class Logic,CollectionIdType,CollectionIdType-method Logic,CollectionType,CollectionType-method MapCollection-class NullCollection-class OMIMCollection-class ontology ontology,GOCollection-method PfamCollection-class PMIDCollection-class PrositeCollection-class setdiff,CollectionIdType,CollectionIdType-method setdiff,CollectionType,CollectionType-method show,BroadCollection-method show,CollectionIdType-method show,CollectionType-method show,GOCollection-method union,CollectionIdType,CollectionIdType-method union,CollectionType,CollectionType-method [,CollectionIdType,missing,missing-method [,GOCollection,missing,missing-method \|,CollectionIdType,CollectionIdType-method \|,CollectionType,CollectionType-method
Methods for Displaying Detailed GeneSet Information	details details,GeneColorSet-method details,GeneSet-method details-methods
Methods to Construct "GeneColorSet" Instances	GeneColorSet GeneColorSet,BroadCollection-method GeneColorSet,character-method GeneColorSet,ExpressionSet-method GeneColorSet,GeneIdentifierType-method GeneColorSet,GeneSet-method GeneColorSet,GOCollection-method GeneColorSet,missing-method GeneColorSet-methods
Class "GeneColorSet"	$,GeneColorSet-method &,GeneColorSet,character-method &,GeneColorSet,GeneColorSet-method coloring coloring,GeneColorSet-method coloring<- coloring<-,GeneColorSet,data.frame-method geneColor geneColor,GeneColorSet-method geneColor<- geneColor<-,GeneColorSet,factor-method GeneColorSet-class initialize,GeneColorSet-method intersect,GeneColorSet,GeneColorSet-method phenotype phenotype,GeneColorSet-method phenotype<- phenotype<-,GeneColorSet,character-method phenotypeColor phenotypeColor,GeneColorSet-method phenotypeColor<- phenotypeColor<-,GeneColorSet,factor-method setdiff,GeneColorSet,GeneColorSet-method show,GeneColorSet-method union,GeneColorSet,GeneColorSet-method [,GeneColorSet,character,ANY-method [,GeneColorSet,numeric,ANY-method [[,GeneColorSet,character-method [[,GeneColorSet,numeric-method \|,GeneColorSet,character-method \|,GeneColorSet,GeneColorSet-method
Gene Identifier Class Constructors	AnnoOrEntrezIdentifier AnnotationIdentifier ENSEMBLIdentifier EntrezIdentifier EnzymeIdentifier GeneIdentifierType GenenameIdentifier GOAllFrameIdentifier KEGGFrameIdentifier NullIdentifier RefseqIdentifier SymbolIdentifier UniprotIdentifier
Class "GeneIdentifierType"	annotation,GeneIdentifierType-method annotation<-,GeneIdentifierType,character-method AnnotationIdentifier-class ENSEMBLIdentifier-class EntrezIdentifier-class EnzymeIdentifier-class GeneIdentifierType-class geneIdType,GeneIdentifierType-method GenenameIdentifier-class GOAllFrameIdentifier-class initialize,GeneIdentifierType-method KEGGFrameIdentifier-class NullIdentifier-class RefseqIdentifier-class show,AnnotationIdentifier-method show,GeneIdentifierType-method SymbolIdentifier-class UniprotIdentifier-class
Methods to construct GeneSet instances	GeneSet GeneSet,BroadCollection-method GeneSet,character-method GeneSet,ExpressionSet-method GeneSet,GeneIdentifierType-method GeneSet,GOCollection-method GeneSet,missing-method GeneSet-methods
Class "GeneSet"	$,GeneSet-method &,GeneSet,character-method &,GeneSet,GeneSet-method collectionType collectionType,GeneSet-method collectionType<- collectionType<-,GeneSet,CollectionType-method contributor contributor,GeneSet-method contributor<- contributor<-,GeneSet,character-method creationDate creationDate,GeneSet-method creationDate<- creationDate<-,GeneSet,character-method description,GeneSet-method description<-,GeneSet,character-method geneIds geneIds,GeneSet-method geneIds<- geneIds<-,GeneSet,character-method geneIdType geneIdType,GeneSet-method geneIdType<- geneIdType<-,GeneSet,character-method geneIdType<-,GeneSet,GeneIdentifierType-method GeneSet-class initialize,GeneSet-method intersect,GeneSet,GeneSet-method Logic,character,GeneSet-method longDescription longDescription,GeneSet-method longDescription<- longDescription<-,GeneSet,character-method organism organism,GeneIdentifierType-method organism,GeneSet-method organism,GOAllFrameIdentifier-method organism,KEGGFrameIdentifier-method organism<- organism<-,GeneSet,character-method pubMedIds,GeneSet-method pubMedIds<-,GeneSet,character-method setdiff,GeneSet,GeneSet-method setIdentifier setIdentifier,GeneSet-method setIdentifier<- setIdentifier<-,GeneSet,character-method setName setName,GeneSet-method setName<- setName<-,GeneSet,character-method setVersion setVersion,GeneSet-method setVersion<- setVersion<-,GeneSet,Versions-method show,GeneSet-method toGmt,GeneSet-method union,GeneSet,GeneSet-method urls urls,GeneSet-method urls<- urls<-,GeneSet,character-method [,ExpressionSet,GeneSet,ANY-method [,GeneSet,character,ANY-method [,GeneSet,numeric,ANY-method [[,GeneSet,character-method [[,GeneSet,numeric-method \|,GeneSet,character-method \|,GeneSet,GeneSet-method
Class "GeneSetCollection"	&,ANY,GeneSetCollection-method &,GeneSetCollection,ANY-method &,GeneSetCollection,GeneSetCollection-method geneIds,GeneSetCollection-method geneIds<-,GeneSetCollection,list-method GeneSetCollection-class intersect,ANY,GeneSetCollection-method intersect,GeneSetCollection,ANY-method Logic,character,GeneSetCollection-method Logic,GeneSet,GeneSetCollection-method names,GeneSetCollection-method setdiff,ANY,GeneSetCollection-method setdiff,GeneSetCollection,ANY-method show,GeneSetCollection-method toGmt,GeneSetCollection-method union,ANY,GeneSetCollection-method union,GeneSetCollection,ANY-method updateObject,GeneSetCollection-method [,GeneSetCollection,character,ANY-method [,GeneSetCollection,logical,ANY-method [,GeneSetCollection,numeric,ANY-method [<-,GeneSetCollection,ANY,ANY,ANY-method [<-,GeneSetCollection,ANY,ANY,GeneSet-method [<-,GeneSetCollection,character,ANY,GeneSet-method [[,GeneSetCollection,character-method [[<-,GeneSetCollection,ANY,ANY,ANY-method [[<-,GeneSetCollection,character,ANY,GeneSet-method [[<-,GeneSetCollection,numeric,ANY,GeneSet-method \|,ANY,GeneSetCollection-method \|,GeneSetCollection,ANY-method \|,GeneSetCollection,GeneSetCollection-method
Methods to construct GeneSetCollection instances	GeneSetCollection GeneSetCollection,character,AnnotationIdentifier,ChrlocCollection-method GeneSetCollection,character,AnnotationIdentifier,CollectionIdType-method GeneSetCollection,character,AnnotationIdentifier,CollectionType-method GeneSetCollection,character,AnnotationIdentifier,GOCollection-method GeneSetCollection,character,AnnotationIdentifier,PfamCollection-method GeneSetCollection,character,AnnotationIdentifier,PrositeCollection-method GeneSetCollection,ExpressionSet,missing,ChrlocCollection-method GeneSetCollection,ExpressionSet,missing,CollectionIdType-method GeneSetCollection,ExpressionSet,missing,CollectionType-method GeneSetCollection,ExpressionSet,missing,GOCollection-method GeneSetCollection,ExpressionSet,missing,KEGGCollection-method GeneSetCollection,ExpressionSet,missing,PfamCollection-method GeneSetCollection,ExpressionSet,missing,PrositeCollection-method GeneSetCollection,GeneSet,missing,missing-method GeneSetCollection,GOAllFrame,missing,GOCollection-method GeneSetCollection,KEGGFrame,missing,KEGGCollection-method GeneSetCollection,list,missing,missing-method GeneSetCollection,missing,AnnotationIdentifier,CollectionIdType-method GeneSetCollection,missing,AnnotationIdentifier,CollectionType-method GeneSetCollection,missing,AnnotationIdentifier,GOCollection-method GeneSetCollection,missing,AnnotationIdentifier,KEGGCollection-method GeneSetCollection-methods
Read OBO-specified Gene Ontology Collections	getOBOCollection
Methods for Function goSlim in Package `GSEABase'	goSlim goSlim,ExpressionSet,GOCollection-method goSlim,GOCollection,GOCollection-method goSlim-methods
Read and write gene sets from Broad or GMT formats	asBroadUri getBroadSets getGmt io toBroadXML toGmt
Methods for Constructing Incidence Matricies Between GeneSets	incidence incidence,GeneSet-method incidence,GeneSetCollection-method incidence-methods
Methods for Function mapIdentifiers in Package `GSEABase'	mapIdentifiers mapIdentifiers,ANY,ANY,ANY-method mapIdentifiers,GeneColorSet,GeneIdentifierType,AnnDbBimap-method mapIdentifiers,GeneColorSet,GeneIdentifierType,environment-method mapIdentifiers,GeneColorSet,GeneIdentifierType,GeneIdentifierType-method mapIdentifiers,GeneColorSet,GeneIdentifierType,NullIdentifier-method mapIdentifiers,GeneColorSet,NullIdentifier,GeneIdentifierType-method mapIdentifiers,GeneSet,GeneIdentifierType,AnnDbBimap-method mapIdentifiers,GeneSet,GeneIdentifierType,environment-method mapIdentifiers,GeneSet,GeneIdentifierType,GeneIdentifierType-method mapIdentifiers,GeneSet,GeneIdentifierType,missing-method mapIdentifiers,GeneSet,GeneIdentifierType,NullIdentifier-method mapIdentifiers,GeneSet,NullIdentifier,GeneIdentifierType-method mapIdentifiers,GeneSetCollection,GeneIdentifierType,missing-method mapIdentifiers-methods
Class "OBOCollection"	coerce,graphNEL,OBOCollection-method coerce,OBOCollection,graphNEL-method OBOCollection-class show,OBOCollection-method subsets subsets,OBOCollection-method [,OBOCollection,character,missing-method