API for lianos/multiGSEA
A unified interface to a plethora of gene set enrichment analysis methods

Global functions
.GeneSetDb Man page
.MultiGSEAResult Man page
GeneSetDb Man page Source code
GeneSetDb-class Man page
GeneSetDb.GeneSetCollection Source code
GeneSetDb.data.frame Source code
GeneSetDb.list Source code
GeneSetDb.list.of.GeneSetCollections Source code
MultiGSEAResult Man page
MultiGSEAResult-class Man page
[,GeneSetDb,ANY,ANY,ANY-method Man page
addCollectionMetadata Man page Source code
addGeneSetMetadata Man page Source code
all.equal.GeneSetDb Man page Source code
annotateGeneSetMembership Man page Source code
append,GeneSetDb,ANY-method Man page
approx.target.from.transformed Source code
as.data.frame Man page
as.data.frame.GeneSetDb Man page Source code
as.list Man page
as.list.GeneSetDb Man page Source code
as_matrix Source code
calculateIndividualLogFC Man page Source code
check.dt Source code
check.gsea.methods Source code
collectionMetadata Man page
conform Man page
conform,GeneSetDb-method Man page
conversion Man page
corplot Man page Source code
csplit Source code
disp.estimated Source code
do.camera Source code
do.cameraPR Source code
do.fgsea Man page Source code
do.fry Source code
do.geneSetTest Source code
do.goseq Man page Source code
do.hyperGeometricTest Man page Source code
do.logFC Source code
do.roast Source code
do.romer Source code
do.scoreSingleSamples.eigenWeightedMean 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
doHyperGInternal Source code
downgradeObject Source code
eigenWeightedMean Man page Source code
encode_gskey Man page Source code
exampleExpressionSet Man page Source code
exampleGeneSetDF Man page Source code
exampleGeneSetDb Man page Source code
exampleGeneSets Man page Source code
exampleMultiGSEAResult Man page Source code
extract.genes Source code
extract_preranked_stats Source code
failWith Man page Source code
fdata Source code
fdata.DGEList Source code
fdata.SummarizedExperiment Source code
fdata.eSet Source code
featureIdMap Man page
featureIdType Man page
featureIdType<- Man page
featureIds Man page
featureIds,GeneSetDb-method Man page
featureIds,MultiGSEAResult-method Man page
geneSet Man page
geneSet,GeneSetDb-method Man page
geneSet,MultiGSEAResult-method Man page
geneSetCollectionURLfunction Man page
geneSetCollectionURLfunction<- Man page
geneSetDb Man page Source code
geneSetSummaryByGenes Man page
geneSetSummaryByGenes,GeneSetDb-method Man page
geneSetSummaryByGenes,MultiGSEAResult-method Man page
geneSetURL Man page
geneSets Man page
geneSets,GeneSetDb-method Man page
geneSetsStats Man page Source code
generate.preranked.stats Source code
getGOslimGeneSetDb Man page Source code
getHousekeepingGeneSetDb Man page Source code
getMSigGeneSetDb Man page Source code
getPantherGOSLIM Source code
getPantherGeneSetDb Man page Source code
getPantherPathways Source code
getReactomeGeneSetDb Man page Source code
goseq Man page Source code
gsd.row.index Source code
gsdScore Man page Source code
gsdlist_conforms_to_gsd Source code
hasGeneSet Man page Source code
hasGeneSetCollection Man page Source code
hyperGeometricTest 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
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
logFC Man page Source code
melt.gs.scores Source code
mg.run Source code
mg_add_points Source code
mgheatmap 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.hyperGeometricTest Source code
mgres.logFC Source code
mgres.roast Source code
mgres.romer Source code
mgres.svdGeneSetTest Source code
msg Man page Source code
multiGSEA Man page Source code
multiGSEA.methods Man page Source code
na.check Source code
onLoad Source code
org Man page
org<- Man page
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.eSet Source code
qiagen.url.fn Source code
readGeneSymbols Source code
rename.feature.columns Source code
rename_rows Man page Source code
rename_rows.DGEList Source code
rename_rows.EList Source code
rename_rows.SummarizedExperiment Source code
rename_rows.bioc Source code
rename_rows.default Source code
rename_rows.df Source code
rename_rows.eSet Source code
resolve.species Source code
result Man page Source code
result.MultiGSEAResult Man page Source code
resultNames Man page Source code
results Man page Source code
scoreSingleSamples 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
summarized 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.full.design Source code
validate.inputs.goseq Source code
validate.inputs.logFC.only Source code
validate.inputs.preranked Source code
validate.x.fry Source code
validate.x.romer Source code
validateCollectionMetadata Source code
validateContrastVector Source code
validateDesign Source code
validateInputs Man page Source code
volcano.source.type Source code
volcanoPlot Man page Source code
volcanoStatsTable Man page Source code
xformGdbForGSVA Source code
zScore Man page Source code
ztransformPvalues Man page Source code
lianos/multiGSEA documentation built on April 10, 2019, 8:38 p.m.