API for rliger
Linked Inference of Genomic Experimental Relationships

Global functions
$.liger	Man page
$<-.liger	Man page
%<>%	Man page
%>%	Man page
.DE.checkDataAvail	Source code
.DataFrame.as.data.frame	Source code
.DollarNames.liger	Source code
.H5AD.checkLayer	Source code
.H5AD.guessDType	Source code
.H5AD.readCSR	Source code
.H5AD.readDense	Source code
.H5AD.readObs	Source code
.H5AD.stringType	Source code
.H5GroupToH5SpMat	Source code
.H_to_conn_mat	Source code
.autoFindRef_qn	Source code
.boolToInt	Source code
.calcEntropy	Source code
.callDESeq2	Source code
.cbind.ligerDataset.h5	Source code
.cbind.ligerDataset.mem	Source code
.centroidAlign.Hraw	Source code
.checkAllDatasets	Source code
.checkArgLen	Source code
.checkCoords	Source code
.checkDatasetVar	Source code
.checkDimReds	Source code
.checkH5LigerDatasetLink	Source code
.checkInit	Source code
.checkInit.mat	Source code
.checkLDSlot	Source code
.checkLigerBarcodes	Source code
.checkLigerDatasetBarcodes	Source code
.checkLigerVarFeature	Source code
.checkObjVersion	Source code
.checkRaster	Source code
.checkUseDatasets	Source code
.checkValidFactorResult	Source code
.cmdDiff	Source code
.collapseLongNames	Source code
.complexHeatmapDotPlot	Man page Source code
.constructHA	Source code
.createMapping	Source code
.deprecateArgs	Source code
.expandDataFrame	Source code
.fetchCellMetaVar	Source code
.fftRtsne	Source code
.findDimRedName	Source code
.formatAnn	Source code
.getSeuratData	Source code
.ggCellViolin	Man page Source code
.ggDensity	Source code
.ggScatter	Man page Source code
.ggplotLigerTheme	Man page Source code
.idxCheck	Source code
.inspectH5Path	Source code
.labelClustBySize	Source code
.log	Source code
.mad	Source code
.makeTextRepr	Source code
.mergeCellMeta	Source code
.onAttach	Source code
.onLoad	Source code
.onUnload	Source code
.pivot_longer	Source code
.plotHeatmap	Man page Source code
.plotSuggestK	Source code
.quantileNorm.HList	Source code
.runCINMF.list	Source code
.runDEG	Source code
.runINMF.list	Source code
.runOnlineINMF.list	Source code
.runUINMF.list	Source code
.same	Source code
.scaleH5SpMatrix	Source code
.selectBatchHVG.by.metric	Source code
.selectGenes.ligerDataset	Source code
.selectGenes.withMetric	Source code
.setColorBarPalette	Source code
.setColorLegendPalette	Source code
.setSeuratData	Source code
.showParam	Source code
.skip	Source code
.splitPeakRegion	Source code
.subsetCellMeta	Source code
.valid.liger	Source code
.valid.ligerATACDataset	Source code
.valid.ligerDataset	Source code
.valid.ligerMethDataset	Source code
.valid.ligerSpatialDataset	Source code
.writeCategroricalToH5AD	Source code
.writeDataFrameToH5AD	Source code
.writeMatrixToH5AD	Source code
.zScore	Source code
ComputeSNN	Source code
DirectSNNToFile	Source code
H5Apply	Man page Source code
RunModularityClusteringCpp	Source code
SLMCluster	Source code
SparseRowVarStd	Source code
WriteEdgeFile	Source code
[.liger	Man page
[.ligerDataset	Man page
[[.liger	Man page
[[<-.liger	Man page
`$.liger`	Source code
`$<-.liger`	Source code
`[.ligerDataset`	Source code
`[.liger`	Source code
`[[.liger`	Source code
`[[<-.liger`	Source code
`names<-.liger`	Source code
alignFactors	Man page Source code
alignFactors.Seurat	Man page Source code
alignFactors.liger	Man page Source code
as.H5Mat.DelayedArray	Source code
as.H5SpMat.DelayedArray	Source code
as.liger	Man page Source code
as.liger.Seurat	Man page Source code
as.liger.SingleCellExperiment	Man page Source code
as.liger.dgCMatrix	Man page Source code
as.ligerDataset	Man page Source code
as.ligerDataset.Seurat	Man page Source code
as.ligerDataset.SingleCellExperiment	Man page Source code
as.ligerDataset.default	Man page Source code
as.ligerDataset.ligerDataset	Man page Source code
as.ligerDataset.matrix	Man page Source code
assign.singletons	Source code
assign.singletons.list	Source code
bmmc	Man page
c.liger	Man page Source code
calcARI	Man page Source code
calcAgreement	Man page Source code
calcAlignment	Man page Source code
calcDatasetSpecificity	Man page Source code
calcGeneVars.H5	Source code
calcNMI	Man page Source code
calcPctInOut	Source code
calcPurity	Man page Source code
cbind.ligerDataset	Man page Source code
ccGeneHuman	Man page
cellMeta	Man page
cellMeta,liger,NULL-method	Man page
cellMeta,liger,character-method	Man page
cellMeta,liger,missing-method	Man page
cellMeta<-	Man page
cellMeta<-,liger,character-method	Man page
cellMeta<-,liger,missing-method	Man page
centroidAlign	Man page Source code
centroidAlign.Seurat	Man page Source code
centroidAlign.liger	Man page Source code
cli_or	Source code
closeAllH5	Man page Source code
closeAllH5.liger	Man page Source code
closeAllH5.ligerDataset	Man page Source code
cluster_vote_rcpp	Source code
colAggregateMedian_dense_cpp	Source code
colAggregateSum_sparse	Source code
colAggregateSums_sparse	Source code
colNNZAggr_sparse	Source code
colNormalize_dense_cpp	Source code
commandDiff	Man page Source code
commands	Man page
commands,liger-method	Man page
computePval	Source code
computeUstat	Source code
convertOldLiger	Man page
coordinate	Man page
coordinate,liger,character-method	Man page
coordinate,ligerSpatialDataset,missing-method	Man page
coordinate<-	Man page
coordinate<-,liger,character-method	Man page
coordinate<-,ligerSpatialDataset,missing-method	Man page
cpp_rank_matrix_dgc	Source code
createH5LigerDataset	Man page Source code
createLiger	Man page Source code
createLigerDataset	Man page Source code
dataset	Man page
dataset,liger,character_OR_NULL-method	Man page
dataset,liger,missing-method	Man page
dataset,liger,numeric-method	Man page
dataset<-	Man page
dataset<-,liger,character,ANY,ANY,matrixLike-method	Man page
dataset<-,liger,character,missing,ANY,NULL-method	Man page
dataset<-,liger,character,missing,ANY,ligerDataset-method	Man page
datasets	Man page
datasets,liger-method	Man page
datasets<-	Man page
datasets<-,liger,logical-method	Man page
datasets<-,liger,missing-method	Man page
defaultCluster	Man page
defaultCluster,liger-method	Man page
defaultCluster<-	Man page
defaultCluster<-,liger,ANY,ANY,NULL-method	Man page
defaultCluster<-,liger,ANY,ANY,character-method	Man page
defaultCluster<-,liger,ANY,ANY,factor-method	Man page
defaultDimRed	Man page
defaultDimRed,liger-method	Man page
defaultDimRed<-	Man page
defaultDimRed<-,liger,character-method	Man page
deg.marker	Man page
deg.pw	Man page
denseZScore	Source code
dim,liger-method	Man page
dim,ligerDataset-method	Man page
dimRed	Man page
dimRed,liger,index-method	Man page
dimRed,liger,missing_OR_NULL-method	Man page
dimRed<-	Man page
dimRed<-,liger,character,ANY,ANY,matrixLike-method	Man page
dimRed<-,liger,index,ANY,ANY,NULL-method	Man page
dimReds	Man page
dimReds,liger-method	Man page
dimReds<-	Man page
dimReds<-,liger,list-method	Man page
dimnames,liger-method	Man page
dimnames,ligerDataset-method	Man page
dimnames<-,liger,list-method	Man page
dimnames<-,ligerDataset,list-method	Man page
downsample	Man page Source code
exportInteractTrack	Man page Source code
extractMergedNormData	Source code
factorGSEA	Man page Source code
factor_cluster_sel	Source code
featureMeta	Man page
featureMeta,ligerDataset-method	Man page
featureMeta<-	Man page
featureMeta<-,ligerDataset-method	Man page
fortify.liger	Man page Source code
fplot	Source code
getFactorMarkers	Man page Source code
getH5File	Man page
getH5File,liger,ANY-method	Man page
getH5File,ligerDataset,missing-method	Man page
getMatrix	Man page
getMatrix,liger,ANY,ANY,ANY-method	Man page
getMatrix,ligerATACDataset,ANY,missing,missing-method	Man page
getMatrix,ligerDataset,ANY,missing,missing-method	Man page
getMode	Source code
getProportionMito	Man page Source code
get_DelayedArray_filepath	Source code
get_DelayedArray_group	Source code
groupSingletons	Source code
gseaSingleGeneSet	Source code
h5fileInfo	Man page
h5fileInfo,ligerDataset-method	Man page
h5fileInfo<-	Man page
h5fileInfo<-,ligerDataset-method	Man page
importBMMC	Man page Source code
importCGE	Man page Source code
importPBMC	Man page Source code
imputeKNN	Man page Source code
inmf_solveH	Source code
inmf_solveV	Source code
inmf_solveW	Source code
is.newLiger	Man page Source code
isH5Liger	Man page Source code
length.liger	Man page Source code
lengths.liger	Man page Source code
liger	Man page
liger-class	Man page
ligerATACDataset	Man page
ligerATACDataset-class	Man page
ligerCommand	Man page
ligerCommand-class	Man page
ligerDataset	Man page
ligerDataset-class	Man page
ligerMethDataset	Man page
ligerMethDataset-class	Man page
ligerRNADataset	Man page
ligerRNADataset-class	Man page
ligerSpatialDataset	Man page
ligerSpatialDataset-class	Man page
ligerToSeurat	Man page Source code
linkGenesAndPeaks	Man page Source code
louvainCluster	Man page Source code
louvainCluster-deprecated	Man page
makeFeatureMatrix	Man page Source code
makeInteractTrack	Man page Source code
makeInteractTrack-deprecated	Man page
makePseudoBulk	Source code
makeRiverplot	Man page Source code
makeRiverplot-deprecated	Man page
mapCellMeta	Man page Source code
max_factor_rcpp	Source code
mergeDenseAll	Man page Source code
mergeH5	Man page Source code
mergeSparseAll	Man page Source code
modalOf	Man page Source code
moe_correct_ridge_cpp	Source code
names.liger	Man page Source code
names<-.liger	Man page
normData	Man page
normData,liger-method	Man page
normData,ligerDataset-method	Man page
normData<-	Man page
normData<-,liger,ANY,ANY,H5D-method	Man page
normData<-,liger,ANY,ANY,matrixLike_OR_NULL-method	Man page
normData<-,ligerDataset,ANY,ANY,H5D-method	Man page
normData<-,ligerDataset,ANY,ANY,matrixLike_OR_NULL-method	Man page
normPeak	Man page
normPeak,liger,character-method	Man page
normPeak,ligerATACDataset,missing-method	Man page
normPeak<-	Man page
normPeak<-,liger,character-method	Man page
normPeak<-,ligerATACDataset,missing-method	Man page
normalize	Man page Source code
normalize.DelayedArray	Man page Source code
normalize.Seurat	Man page Source code
normalize.dgCMatrix	Man page Source code
normalize.liger	Man page Source code
normalize.ligerDataset	Man page Source code
normalize.matrix	Man page Source code
normalizePeak	Man page Source code
normalize_byCol_dense_rcpp	Source code
objErr_i	Source code
online_iNMF	Man page Source code
online_iNMF-deprecated	Man page
optimizeALS	Man page Source code
optimizeALS-deprecated	Man page
optimizeNewData	Man page Source code
optimizeNewK	Man page Source code
optimizeNewLambda	Man page Source code
optimizeSubset	Man page Source code
pbmc	Man page
pbmcPlot	Man page
plot.factorGSEA	Man page Source code
plotBarcodeRank	Man page Source code
plotByDatasetAndCluster	Man page Source code
plotCellViolin	Man page Source code
plotClusterDimRed	Man page Source code
plotClusterFactorDot	Man page Source code
plotClusterGeneDot	Man page Source code
plotClusterGeneViolin	Man page Source code
plotClusterProportions	Man page Source code
plotDatasetDimRed	Man page Source code
plotDensityDimRed	Man page Source code
plotDimRed	Man page Source code
plotEnhancedVolcano	Man page Source code
plotFactorDimRed	Man page Source code
plotFactorHeatmap	Man page Source code
plotGODot	Man page Source code
plotGeneDetectedViolin	Man page Source code
plotGeneDimRed	Man page Source code
plotGeneHeatmap	Man page Source code
plotGeneLoadingRank	Man page Source code
plotGeneLoadings	Man page Source code
plotGeneViolin	Man page Source code
plotGroupClusterDimRed	Man page Source code
plotMarkerHeatmap	Man page Source code
plotPairwiseDEGHeatmap	Man page Source code
plotPeakDimRed	Man page Source code
plotProportion	Man page Source code
plotProportionBar	Man page Source code
plotProportionBox	Man page Source code
plotProportionDot	Man page Source code
plotProportionPie	Man page Source code
plotSankey	Man page Source code
plotSpatial2D	Man page Source code
plotSpatial2D.liger	Man page Source code
plotSpatial2D.ligerSpatialDataset	Man page Source code
plotTotalCountViolin	Man page Source code
plotVarFeatures	Man page Source code
plotVolcano	Man page Source code
print.factorGSEA	Man page Source code
quantileAlignSNF	Man page Source code
quantileNorm	Man page Source code
quantileNorm.Seurat	Man page Source code
quantileNorm.liger	Man page Source code
quantile_norm	Man page Source code
quantile_norm-deprecated	Man page
rawData	Man page
rawData,liger-method	Man page
rawData,ligerDataset-method	Man page
rawData<-	Man page
rawData<-,liger,ANY,ANY,H5D-method	Man page
rawData<-,liger,ANY,ANY,matrixLike_OR_NULL-method	Man page
rawData<-,ligerDataset,ANY,ANY,H5D-method	Man page
rawData<-,ligerDataset,ANY,ANY,matrixLike_OR_NULL-method	Man page
rawPeak	Man page
rawPeak,liger,character-method	Man page
rawPeak,ligerATACDataset,missing-method	Man page
rawPeak<-	Man page
rawPeak<-,liger,character-method	Man page
rawPeak<-,ligerATACDataset,missing-method	Man page
read10X	Man page Source code
read10XATAC	Man page Source code
read10XFiles	Man page Source code
read10XH5	Man page Source code
read10XH5Delay	Man page Source code
read10XH5Mem	Man page Source code
read10XRNA	Man page Source code
readH5AD	Man page Source code
readH5ADDelay	Man page Source code
readH5ADMem	Man page Source code
readLiger	Man page Source code
readSubset	Man page Source code
recordCommand	Source code
reexports	Man page
removeMissing	Man page Source code
removeMissingObs	Man page Source code
restoreH5Liger	Man page Source code
restoreOnlineLiger	Man page Source code
retrieveCellFeature	Man page Source code
reverseMethData	Man page Source code
rliger	Man page
rliger-deprecated	Man page
rliger-package	Man page
rowAggregateSum_sparse	Source code
rowDivide_rcpp	Source code
rowNNZAggr_sparse	Source code
rowVarsDense	Source code
rowVars_sparse_rcpp	Source code
runCINMF	Man page Source code
runCINMF.Seurat	Man page Source code
runCINMF.liger	Man page Source code
runCluster	Man page Source code
runGOEnrich	Man page Source code
runGSEA	Man page Source code
runGeneralQC	Man page Source code
runGeneralQC.DelayedH5	Source code
runGeneralQC.Matrix	Source code
runGeneralQC.h5	Source code
runINMF	Man page Source code
runINMF.Seurat	Man page Source code
runINMF.liger	Man page Source code
runIntegration	Man page Source code
runIntegration.Seurat	Man page Source code
runIntegration.liger	Man page Source code
runMarkerDEG	Man page Source code
runOnlineINMF	Man page Source code
runOnlineINMF.Seurat	Man page Source code
runOnlineINMF.liger	Man page Source code
runPairwiseDEG	Man page Source code
runTSNE	Man page Source code
runUINMF	Man page Source code
runUINMF.liger	Man page Source code
runUMAP	Man page Source code
runWilcoxon	Man page Source code
safeH5Create	Source code
safe_scale	Source code
sample_cpp	Source code
scaleData	Man page
scaleData,liger,ANY-method	Man page
scaleData,ligerDataset,missing-method	Man page
scaleData<-	Man page
scaleData<-,liger,ANY,ANY,H5D-method	Man page
scaleData<-,liger,ANY,ANY,H5Group-method	Man page
scaleData<-,liger,ANY,ANY,matrixLike_OR_NULL-method	Man page
scaleData<-,ligerDataset,ANY,ANY,H5D-method	Man page
scaleData<-,ligerDataset,ANY,ANY,H5Group-method	Man page
scaleData<-,ligerDataset,ANY,ANY,matrixLike_OR_NULL-method	Man page
scaleL2norm	Source code
scaleNotCenter	Man page Source code
scaleNotCenter.DelayedArray	Man page Source code
scaleNotCenter.Seurat	Man page Source code
scaleNotCenter.dgCMatrix	Man page Source code
scaleNotCenter.liger	Man page Source code
scaleNotCenter.ligerDataset	Man page Source code
scaleNotCenter.ligerMethDataset	Man page Source code
scaleNotCenter_byCol_dense_rcpp	Source code
scaleNotCenter_byRow_perDataset_rcpp	Source code
scaleNotCenter_byRow_rcpp	Source code
scaleUnsharedData	Man page
scaleUnsharedData,liger,character-method	Man page
scaleUnsharedData,liger,numeric-method	Man page
scaleUnsharedData,ligerDataset,missing-method	Man page
scaleUnsharedData<-	Man page
scaleUnsharedData<-,liger,ANY,ANY,H5D-method	Man page
scaleUnsharedData<-,liger,ANY,ANY,H5Group-method	Man page
scaleUnsharedData<-,liger,ANY,ANY,matrixLike_OR_NULL-method	Man page
scaleUnsharedData<-,ligerDataset,missing,ANY,H5D-method	Man page
scaleUnsharedData<-,ligerDataset,missing,ANY,H5Group-method	Man page
scaleUnsharedData<-,ligerDataset,missing,ANY,matrixLike_OR_NULL-	Man page
searchH	Source code
selectBatchHVG	Man page Source code
selectBatchHVG.DelayedArray	Man page Source code
selectBatchHVG.dgCMatrix	Man page Source code
selectBatchHVG.liger	Man page Source code
selectBatchHVG.ligerDataset	Man page Source code
selectGenes	Man page Source code
selectGenes.Seurat	Man page Source code
selectGenes.liger	Man page Source code
selectGenesVST	Man page Source code
setupRepVar	Source code
seuratToLiger	Man page
show,liger-method	Man page
show,ligerCommand-method	Man page
show,ligerDataset-method	Man page
sparse.transpose	Source code
sparse.var	Source code
splitRmMiss	Source code
sub-liger	Man page
sub-ligerDataset	Man page
sub-sub-liger	Man page
subsetH5LigerDataset	Man page Source code
subsetH5LigerDatasetToH5	Source code
subsetH5LigerDatasetToMem	Source code
subsetLiger	Man page Source code
subsetLigerDataset	Man page Source code
subsetMemLigerDataset	Man page Source code
suggestK	Man page Source code
sumSquaredDeviations	Source code
summary.factorGSEA	Man page Source code
updateLigerObject	Man page Source code
updateNCellExprRcpp	Source code
updateOldLiger	Source code
updatePseudoBulkRcpp	Source code
updateRliger2NS	Source code
varFeatures	Man page
varFeatures,liger-method	Man page
varFeatures<-	Man page
varFeatures<-,liger,ANY,character-method	Man page
varUnsharedFeatures	Man page
varUnsharedFeatures,liger,ANY-method	Man page
varUnsharedFeatures,ligerDataset,missing-method	Man page
varUnsharedFeatures<-	Man page
varUnsharedFeatures<-,liger,ANY,ANY,character-method	Man page
varUnsharedFeatures<-,ligerDataset,missing,ANY,character-method	Man page
wilcoxauc	Source code
writeH5	Man page Source code
writeH5.default	Man page Source code
writeH5.dgCMatrix	Man page Source code
writeH5.liger	Man page Source code
writeH5.ligerDataset	Man page Source code
writeH5AD	Man page Source code
writeH5AD.dgCMatrix	Man page Source code
writeH5AD.liger	Man page Source code
writeH5AD.ligerDataset	Man page Source code