lianos/sparrow
Take command of set enrichment analyses through a unified interface

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313
Source code
85
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59
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lianos/sparrow: Take command of set enrichment analyses through a unified interface
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API

API for lianos/sparrow
Take command of set enrichment analyses through a unified interface

Global functions
.GeneSetDb Man page
.GeneSetDb.list.of.GeneSetCollections Source code
.SparrowResult Man page
.approx_target_from_transformed Source code
.geneSetURL.GOSLIM Source code
.geneSetURL.KEGG Source code
.geneSetURL.NA Source code
.geneSetURL.PANTHERpathway Source code
.geneSetURL.REACTOME Source code
.geneSetURL.msigdb Source code
.get_kegg_pathway_db Source code
.gsd.row.index Source code
.gsdlist_conforms_to_gsd Source code
.looks0centered Source code
.onLoad Source code
.prep_babelgene_table Source code
.renameRows.bioc Source code
.renameRows.df Source code
.replace Source code
.target_column_idxs Source code
.validate.inputs.full.design Source code
.validate.inputs.logFC.only Source code
.validate.inputs.preranked Source code
.validateCollectionMetadata Source code
.validateContrastVector Source code
.validateDesign Source code
.volcano_source_type Source code
GeneSetDb Man page Source code
GeneSetDb-class Man page
GeneSetDb.BiocSet Source code
GeneSetDb.GeneSetCollection Source code
GeneSetDb.GeneSetDb Source code
GeneSetDb.data.frame Source code
GeneSetDb.default Source code
GeneSetDb.list Source code
SparrowResult Man page
SparrowResult-class Man page
[,GeneSetDb,ANY,ANY,ANY-method Man page
`fdata<-.DGEList` Source code
`fdata<-.SummarizedExperiment` Source code
`fdata<-.eSet` Source code
`fdata<-` Source code
`pdata<-.DGEList` Source code
`pdata<-.EList` Source code
`pdata<-.SummarizedExperiment` Source code
`pdata<-.eSet` Source code
`pdata<-` Source code
addCollectionMetadata Man page Source code
addGeneSetMetadata Man page Source code
all.equal.GeneSetDb Man page Source code
annotateGeneSetMembership Man page Source code
as.data.frame Man page
as.data.frame.GeneSetDb Man page Source code
as.data.table Man page
as.data.table.GeneSetDb Man page Source code
as.list Man page
as.list.GeneSetDb Source code
as_matrix Source code
calculateIndividualLogFC Man page Source code
check.dt Source code
check.gsea.methods Source code
collectionMetadata Man page
collectionMetadata,GeneSetDb,character,character-method Man page
collectionMetadata,GeneSetDb,character,missing-method Man page
collectionMetadata,GeneSetDb,missing,missing-method Man page
combine,GeneSetDb,GeneSetDb-method Man page
combine,SparrowResult,SparrowResult-method Man page
conform Man page
conform,GeneSetDb-method Man page
conversion Man page
convertIdentifiers Man page
convertIdentifiers,BiocSet-method Man page
convertIdentifiers,GeneSetDb-method Man page
corplot Man page Source code
csplit Source code
disp.estimated Source code
do.camera Source code
do.cameraPR Source code
do.fgsea Source code
do.fry Source code
do.geneSetTest Source code
do.goseq Source code
do.logFC Source code
do.ora Source code
do.roast Source code
do.romer Source code
do.scoreSingleSamples.eigenWeightedMean Source code
do.scoreSingleSamples.ewzscore Source code
do.scoreSingleSamples.gsd Source code
do.scoreSingleSamples.gsva Source code
do.scoreSingleSamples.mean Source code
do.scoreSingleSamples.zscore Source code
do.svdGeneSetTest Source code
downgradeObject Source code
eigenWeightedMean Man page Source code
encode_gskey Man page Source code
exampleBiocSet Man page Source code
exampleDgeResult Man page Source code
exampleExpressionSet Man page Source code
exampleGeneSetDF Man page Source code
exampleGeneSetDb Man page Source code
exampleGeneSets Man page Source code
exampleSparrowResult Man page Source code
extract_preranked_stats Source code
failWith Man page Source code
fdata Source code
fdata.DGEList Source code
fdata.SummarizedExperiment Source code
fdata.default Source code
fdata.eSet Source code
featureIdMap Man page
featureIdMap,GeneSetDb-method Man page
featureIdType Man page
featureIdType,GeneSetDb-method Man page
featureIdType<- Man page
featureIdType<-,GeneSetDb-method Man page
featureIds Man page
featureIds,GeneSetDb-method Man page
featureIds,SparrowResult-method Man page
geneSet Man page
geneSet,GeneSetDb-method Man page
geneSet,SparrowResult-method Man page
geneSetCollectionURLfunction Man page
geneSetCollectionURLfunction,GeneSetDb-method Man page
geneSetCollectionURLfunction,SparrowResult-method Man page
geneSetCollectionURLfunction<- Man page
geneSetCollectionURLfunction<-,GeneSetDb-method Man page
geneSetDb Man page Source code
geneSetSummaryByGenes Man page
geneSetSummaryByGenes,GeneSetDb-method Man page
geneSetSummaryByGenes,SparrowResult-method Man page
geneSetURL Man page
geneSetURL,GeneSetDb-method Man page
geneSetURL,SparrowResult-method Man page
geneSets Man page
geneSets,GeneSetDb-method Man page
geneSets,SparrowResult-method Man page
geneSetsStats Man page Source code
generate.preranked.stats Source code
getKeggCollection Man page Source code
getKeggGeneSetDb Man page Source code
getMSigCollection Man page Source code
getMSigGeneSetDb Man page Source code
getPantherCollection Man page Source code
getPantherGOSLIM Source code
getPantherGeneSetDb Man page Source code
getPantherPathways Source code
getReactomeCollection Man page Source code
getReactomeGeneSetDb Man page Source code
get_function Source code
goseq Man page Source code
gsdScore Man page Source code
hasGeneSet Man page Source code
hasGeneSetCollection Man page Source code
incidenceMatrix Man page Source code
init.gsd.db.from.list.of.lists Source code
init.gsd.table.from.db Source code
invalidMethods Source code
iplot Man page Source code
iplot.boxplot.plotly Source code
iplot.density.plotly Source code
iplot.gsea.plot Source code
is.active Man page Source code
is.conformed Man page Source code
is.logFC.like Source code
is.single.list.of.feature.vectors Source code
isSingleCharacter Source code
isSingleInteger Source code
isSingleLogical Source code
isSingleNumeric Source code
length,GeneSetDb-method Man page
logFC Man page Source code
melt.gs.scores Source code
mg.run Source code
mg_add_points Source code
mgheatmap Man page Source code
mgheatmap2 Man page Source code
mgres.camera Source code
mgres.fgsea Source code
mgres.fry Source code
mgres.geneSetTest Source code
mgres.goseq Source code
mgres.logFC Source code
mgres.ora Source code
mgres.roast Source code
mgres.romer Source code
mgres.svdGeneSetTest Source code
msg Man page Source code
na.check Source code
nrow,GeneSetDb-method Man page
ora Man page Source code
p.matrix Man page Source code
panel.cor Source code
panel.hist Source code
panel.spoints Source code
pdata Source code
pdata.DGEList Source code
pdata.EList Source code
pdata.SummarizedExperiment Source code
pdata.default Source code
pdata.eSet Source code
plot_ora_bias Man page Source code
randomGeneSetDb Man page Source code
readGeneSymbols Source code
rename.feature.columns Source code
renameCollections Man page Source code
renameRows Man page Source code
renameRows.DGEList Source code
renameRows.EList Source code
renameRows.SummarizedExperiment Source code
renameRows.default Source code
renameRows.eSet Source code
reqpkg Source code
resolve.species Source code
result Man page Source code
result.SparrowResult Man page Source code
resultNames Man page Source code
results Man page Source code
scale_rows Man page Source code
scale_rows.Matrix Source code
scale_rows.default Source code
scale_rows.matrix Source code
scale_rows.sparseMatrix Source code
scoreSingleSamples Man page Source code
seas Man page Source code
sparrow_methods Man page Source code
species_info Man page Source code
split_gskey Man page Source code
ssGSEA.normalize Man page Source code
subset.GeneSetDb Man page Source code
subsetByFeatures Man page
subsetByFeatures,GeneSetDb-method Man page
tabulateResults Man page Source code
unconform Man page
unconform,GeneSetDb-method Man page
validate.DGEList Source code
validate.X Source code
validate.XwithWeights Source code
validate.gene.sets.input Source code
validate.inputs.goseq Source code
validate.inputs.ora Source code
validate.x.fry Source code
validate.x.romer Source code
validate.xmeta Source code
validateInputs Man page Source code
volcanoPlot Man page Source code
volcanoStatsTable Man page Source code
zScore Man page Source code
ztransformPvalues Source code
lianos/sparrow documentation built on Feb. 5, 2024, 2:58 p.m.

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