Analysis Tools for scATACseq Data with CoGAPS

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Documentation for package ‘ATACCoGAPS’ version 1.6.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

applyGREAT	Find Enrichment of GO Terms in PatternMarker Peaks using GREAT
ATACTransferLearning	Transfer Learning between ATACseq data sets using projectR
cgapsPlot	Plot Individual CoGAPS Patterns
dataSubsetBySparsity	Filter scATACseq by sparsity
exampleMotifList	Example list of motifs for examples
findRegulatoryNetworks	Find Motifs and TFs from PatternMarker Peaks
foldAccessibility	Estimate fold Accessibility of a Gene Relative to Average
geneAccessibility	Find the accessibility of the peaks overlapping a set of genes and their promoters
genePatternMatch	Match genes to pattern differentiating peaks
getTFDescriptions	Find Motifs and TFs from PatternMarker Peaks
getTFs	Find Motifs and TFs from PatternMarker Peaks
heatmapGeneAccessibility	Heatmap Gene Accessibility
heatmapPatternMarkers	Create Heatmap of PatternMarker Peaks
heatmapPatternMatrix	Plot the patternMatrix as a heatmap
motifPatternMatch	Find Motifs and TFs from PatternMarker Peaks
motifSummarization	Map Peaks to DNA motifs in scATAC-seq Data
pathwayMatch	Matches list of genes to pathways
patternMarkerCellClassifier	Match cells to patterns
peaksToGRanges	List of peaks to GRanges
RNAseqTFValidation	Validate TF Findings with RNA-seq CoGAPS
schepCellTypes	Cell types corresponding to subsetSchepData
schepCogapsResult	CogapsResult from the subsetSchepData object
schepGranges	GRanges corresponding to subsetSchepData
schepPeaks	Peaks corresponding to subsetSchepData
simpleMotifTFMatch	Motif/TF Matching in a Single Function
subsetSchepData	Small subset of the scATAC-seq data from Schep et al, 2017, Nature Methods paper.
tfData	List of human TFs and motifs from cisBP database