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"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" ] }, { "page": "getOBOCollection", "title": "Read OBO-specified Gene Ontology Collections", "topics": [ "getOBOCollection" ] }, { "page": "goSlim-methods", "title": "Methods for Function goSlim in Package `GSEABase'", "topics": [ "goSlim", "goSlim,ExpressionSet,GOCollection-method", "goSlim,GOCollection,GOCollection-method", "goSlim-methods" ] }, { "page": "getObjects", "title": "Read and write gene sets from Broad or GMT formats", "topics": [ "asBroadUri", "getBroadSets", "getGmt", "io", "toBroadXML", "toGmt" ] }, { "page": "incidence-methods", "title": "Methods for Constructing Incidence Matricies Between GeneSets", "topics": [ "incidence", "incidence,GeneSet-method", "incidence,GeneSetCollection-method", "incidence-methods" ] }, { "page": "mapIdentifiers-methods", "title": "Methods for Function mapIdentifiers in Package `GSEABase'", "topics": [ "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" ] }, { "page": "OBOCollection-class", "title": "Class \"OBOCollection\"", "topics": [ "coerce,graphNEL,OBOCollection-method", "coerce,OBOCollection,graphNEL-method", "OBOCollection-class", "show,OBOCollection-method", "subsets", "subsets,OBOCollection-method", "[,OBOCollection,character,missing-method" ] } ], "_rundeps": [ "annotate", "AnnotationDbi", "askpass", "Biobase", "BiocBaseUtils", "BiocGenerics", "Biostrings", "bit", "bit64", "blob", "cachem", "cli", "cpp11", "crayon", "curl", "DBI", "fastmap", "generics", "glue", "graph", "httr", "IRanges", "jsonlite", "KEGGREST", "lifecycle", "memoise", "mime", "openssl", "pkgconfig", "png", "R6", "rlang", "RSQLite", "S4Vectors", "Seqinfo", "sys", "vctrs", "XML", "xtable", "XVector" ], "_vignettes": [ { "source": "GSEABase.Rmd", "filename": "GSEABase.html", "title": "An introduction to GSEABase", "author": "Martin Morgan, Paul Villafuerte", "engine": "knitr::rmarkdown", "headings": [ "GeneSet", "GeneColorSet", "GeneSetCollection" ], "created": "2023-02-24 21:10:07", "modified": "2023-02-24 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