Man pages for FertigLab/ATACCoGAPS
Analysis Tools for scATACseq Data with CoGAPS
| applyGREAT | Find Enrichment of GO Terms in PatternMarker Peaks using... |
| 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 |
| foldAccessibility | Estimate fold Accessibility of a Gene Relative to Average |
| geneAccessibility | Find the accessibility of the peaks overlapping a set of... |
| genePatternMatch | Match genes to pattern differentiating 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,... |
| tfData | List of human TFs and motifs from cisBP database |
