GeneSetDb-class         A container for geneset definitions.
SparrowResult-class     A SparrowResult object holds the results from a
                        sparrow::seas() call.
[,GeneSetDb,ANY,ANY,ANY-method
                        Subset whole genesets from a GeneSetDb
addGeneSetMetadata      Add metadata at the geneset level.
all.equal.GeneSetDb     Checks equality (feature parity) between
                        GeneSetDb objects
annotateGeneSetMembership
                        Annotates rows of a data.frame with geneset
                        membership from a GeneSetDb
calculateIndividualLogFC
                        Utility function to run limma differential
                        expression analysis
collectionMetadata      Gene Set Collection Metadata
combine,GeneSetDb,GeneSetDb-method
                        Combines two GeneSetDb objects together
combine,SparrowResult,SparrowResult-method
                        Combines two SparrowResult objects together.
conform                 (Re)-map geneset IDs to the rows in an
                        expression object.
conversion              Convert a GeneSetDb to other formats.
convertIdentifiers      Converts internal feature identifiers in a
                        GeneSetDb to a set of new ones.
corplot                 Plots the correlation among the columns of a
                        numeric matrix.
eigenWeightedMean       Single sample gene set score by a weighted
                        average of the genes in geneset
encode_gskey            Converts collection,name combination to key for
                        geneset
exampleExpressionSet    Functions that load data for use in examples
                        and testing.
failWith                Utility function to try and fail with grace.
featureIdMap            Fetch the featureIdMap for a 'GeneSetDb'
featureIds              Returns the relevant featureIds for a given
                        geneset.
geneSet                 Fetches information for a gene set
geneSetCollectionURLfunction
                        Get/set the gene set collection url function
                        for a geneset collection
geneSetDb               Fetches the GeneSetDb from SparrowResult
geneSetSummaryByGenes   Summarize geneset:feature relationships for
                        specified set of features
geneSets                Fetch the active (or all) gene sets from a
                        GeneSetDb or SparrowResult
geneSetsStats           Summarizes useful statistics per gene set from
                        a SparrowResult
getKeggCollection       Retrieves the KEGG gene set collection via its
                        REST API
getMSigCollection       Fetches gene set collections from the moleular
                        signature database (MSigDB)
getPantherCollection    Get pathways/GOslim collections from PANTHER.db
                        Biocondcutor package.
getReactomeCollection   Retrieve gene set collections from from
                        reactome.db
goseq                   Perform goseq Enrichment tests across a
                        GeneSetDb.
gsdScore                Single sample geneset score using SVD based
                        eigengene value per sample.
hasGeneSet              Check to see if the GeneSetDb has a
                        collection,name GeneSet defined
hasGeneSetCollection    Check if a collection exists in the 'GeneSetDb'
incidenceMatrix         Creates a 1/0 matrix to indicate geneset
                        membership to target object.
iplot                   Visualize gene level behavior of genes within a
                        geneset across a contrast.
is.active               Interrogate "active" status of a given geneset.
logFC                   Extract the individual fold changes statistics
                        for elements in the expression object.
mgheatmap               Creates a "geneset smart"
                        ComplexHeatmap::Heatmap
mgheatmap2              Creates a "geneset smart"
                        ComplexHeatmap::Heatmap
msg                     Utility function to cat a message to stderr (by
                        default)
ora                     Performs an overrepresentation analysis,
                        (optionally) accounting for bias.
p.matrix                Assembles a matrix of nominal or adjusted
                        pvalues from a sparrow::seas result
randomGeneSetDb         Generates a fake GeneSetDb by sampling from
                        features in a seas input.
renameCollections       Rename the collections in a GeneSetDb
renameRows              Smartly/easily rename the rows of an object.
resultNames             Interrogate the results of a sparrow::seas
                        analysis stored in a SparrowResult
scale_rows              Centers and scales the rows of a numeric
                        matrix.
scoreSingleSamples      Generates single sample gene set scores across
                        a datasets by many methods
seas                    Performs a plethora of set enrichment analyses
                        over varied inputs.
sparrow_methods         Lists the supported GSEA methods by sparrow
species_info            Match a species query to the regularized
                        species info.
ssGSEA.normalize        Normalize a vector of ssGSEA scores in the
                        ssGSEA way.
subset.GeneSetDb        Subset GeneSetDb to only include specified
                        genesets.
subsetByFeatures        Subset a GeneSetDb to only include geneSets
                        with specified features.
validateInputs          Validate the input objects to a GSEA call.
volcanoPlot             Create an interactive volcano plot
volcanoStatsTable       Extracts x and y axis values from objects to
                        create input for volcano plot
zScore                  Calculate single sample geneset score by
                        average z-score method
