# Analysis Tools for scATACseq Data with CoGAPS

## Documentation for package ‘ATACCoGAPS’ version 1.0.0

- 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