.callOpenTiles_ArchR |
'callOpenTiles' Perform peak-calling on a set of fragments or an ArchR Project. |
.counts_plot_default_theme |
Default ggplot theme for counts plot |
.gene_plot_theme |
Common theme for gene plots |
addAccessibilityShift |
'addAccessibilityShift' |
addMotifSet |
'addMotifSet' |
annotateTiles |
'annotateTiles' |
bulkDimReduction |
'bulkDimReduction' |
bulkUMAP |
'bulkUMAP' |
callOpenTiles |
'callOpenTiles' Perform peak-calling on a set of fragments or an ArchR Project. |
callOpenTiles-method |
'callOpenTiles' Perform peak-calling on a set of fragments or an ArchR Project. |
combineSampleTileMatrix |
'combineSampleTileMatrix' |
differentialsToGRanges |
'differentialsToGRanges' Converts a data.frame matrix to a GRanges, preserving additional columns as GRanges metadata |
exampleBlackList |
exampleBlackList |
exampleCellColData |
exampleCellColData |
exampleFragments |
exampleFragments |
exportCoverage |
'exportCoverage' |
exportDifferentials |
'exportDifferentials' |
exportMotifs |
'exportMotifs' |
exportOpenTiles |
'exportOpenTiles' |
exportSmoothedInsertions |
'exportSmoothedInsertions' |
extractRegion |
'extractRegion' |
filterCoAccessibleLinks |
'filterCoAccessibleLinks' |
finalModelObject |
finalModelObject |
getAltTSS |
Annotate Peaks falling in Transcription Start Sites (TSS) and identify alternatively regulated TSSs for each gene. |
getAnnotationDbFromInstalledPkgname |
'getAnnotationDbFromInstalledPkgname' Loads and attaches an installed TxDb or OrgDb-class Annotation database package. |
getCellPopMatrix |
'getCellPopMatrix' |
getCellTypes |
'getCellTypes' Extract cell type names from a Tile Results or Sample Tile object. |
getCellTypeTiles |
'getCellTypeTiles' Extract the GRanges for a particular cell type |
getCoAccessibleLinks |
'getCoAccessibleLinks' |
getCoverage |
Get sample-specific coverage files for each sample-cell population. |
getDifferentialAccessibleTiles |
'getDifferentialAccessibleTiles' |
getIntensityThreshold |
'getIntensityThreshold' |
getModelValues |
getModelValues from runZIGLMM output. |
getPopFrags |
Extract fragments by populations from an ArchR Project |
getPromoterGenes |
'getPromoterGenes' |
getSampleCellTypeMetadata |
'getSampleCellTypeMetadata' Extract Sample-celltype specific metadata |
getSampleTileMatrix |
'getSampleTileMatrix' |
getSequencingBias |
'getSequencingBias' |
GRangesToString |
'GRangesToString' Converts a GRanges object to a string in the format 'chr1:100-200' |
mergeTileResults |
'mergeTileResults' |
MotifEnrichment |
'MotifEnrichment' |
MotifSetEnrichmentAnalysis |
'MotifSetEnrichmentAnalysis' |
packMOCHA |
'packMOCHA' |
pilotLMEM |
Execute a pilot run of single linear model on a subset of data |
pilotZIGLMM |
Execute a pilot run of model on a subset of data |
plotConsensus |
'plotConsensus' |
plotIntensityDistribution |
'plotIntensityDistribution' |
plotRegion |
'plotRegion' |
renameCellTypes |
'renameCellTypes' |
runLMEM |
Run Linear Mixed-Effects Modeling for continuous, non-zero inflated data |
runZIGLMM |
Run Zero-inflated Generalized Linear Mixed Modeling on pseudobulked scATAC data |
StringsToGRanges |
'StringsToGRanges' |
subsetMOCHAObject |
'subsetMOCHAObject' |
testCoAccessibility |
'testCoAccessibility' |
unpackMOCHA |
'unpackMOCHA' |
varZIGLMM |
Zero-inflated Variance Decomposition for pseudobulked scATAC data |
youden_threshold |
youden_threshold |