Man pages for FertigLab/ATACCoGAPS
Analysis Tools for scATACseq Data with CoGAPS

applyGREATFind Enrichment of GO Terms in PatternMarker Peaks using...
ATACTransferLearningTransfer Learning between ATACseq data sets using projectR
cgapsPlotPlot Individual CoGAPS Patterns
dataSubsetBySparsityFilter scATACseq by sparsity
exampleMotifListExample list of motifs for examples
foldAccessibilityEstimate fold Accessibility of a Gene Relative to Average
geneAccessibilityFind the accessibility of the peaks overlapping a set of...
genePatternMatchMatch genes to pattern differentiating peaks
heatmapGeneAccessibilityHeatmap Gene Accessibility
heatmapPatternMarkersCreate Heatmap of PatternMarker Peaks
heatmapPatternMatrixPlot the patternMatrix as a heatmap
motifPatternMatchFind Motifs and TFs from PatternMarker Peaks
motifSummarizationMap Peaks to DNA motifs in scATAC-seq Data
pathwayMatchMatches list of genes to pathways
patternMarkerCellClassifierMatch cells to patterns
peaksToGRangesList of peaks to GRanges
RNAseqTFValidationValidate TF Findings with RNA-seq CoGAPS
schepCellTypesCell types corresponding to subsetSchepData
schepCogapsResultCogapsResult from the subsetSchepData object
schepGrangesGRanges corresponding to subsetSchepData
schepPeaksPeaks corresponding to subsetSchepData
simpleMotifTFMatchMotif/TF Matching in a Single Function
subsetSchepDataSmall subset of the scATAC-seq data from Schep et al, 2017,...
tfDataList of human TFs and motifs from cisBP database
FertigLab/ATACCoGAPS documentation built on Feb. 8, 2023, 6:46 p.m.