Man pages for huqiwen0313/snarePip
snarePip
| addAtacObj | Creat additional slots for atac-seq analysis extended from an... |
| addMotifMatrix | generate motif to feature(peak) matrix, row motifs, column... |
| alignmentStat | caculate alignment statistics |
| assignPeakToGene | asssign peak to its nearest gene |
| calDoubletScore | calculate score for potential doublet |
| calJaccard | calculate jaccard index between two binary matrices |
| callMACs | call peaks based on macs2 obj: p2 object record the fragment... |
| callMACsCluster | call peaks based on assigned cell clusters |
| cellStatistics | calculate QC statistics per each cell blacklist ratio,... |
| ciceroGeneActivity | calculate cicero gene activity score |
| createInputCDS | creating input CDS from custom peaks |
| dimReduct | run dimension reduction |
| enrichMotifs | identify enriched motifs for a feature set (peaks) based on... |
| enrichMotifsDAR | identify overrepresentative motifs in DAR regions for each... |
| fragmentOverlapPeaks | Caculate the number of fragment that overlapped with peak... |
| fragmentOverlapPeaksPlot | plot fragment overlap peaks |
| GetMarkerExprMatrix | Get gene expression matrix of associated marker genes |
| hvgPeaks | calculate high variable peaks based on normalized cell by... |
| idenDAR | identify differential accessible region based on pagoda... |
| intPosMat | generate integrated cell position matrix given sets of... |
| normJD | normalize jaccard index matrix based on fang et al doi:... |
| normPmatrix | normalize peak matrix based on TF-IDF and other algorithms |
| plotAssoGenes | plot heatmap of associated genes |
| plotComponentVariancePagoda | plotComponentVariance based on pagoda obj |
| plotDARoverlap | plot distribution of DAR overlapping with annotated regions |
| plotFeature | plot features based on embedding for individual cluster |
| plotFragmentScatter | plotting fragment distribution Scatterplot showing the number... |
| plotSaturation | plot saturation |
| plotSnareBarcodeComparison | plot the comparison between RNA and ATAC barcode |
| plotTopMotifs | plot top motifs for each cluster |
| posMatrix | Generate cell position matrix in a given region based on... |
| PrepareFragmentPlot | prepare data frame for plotting |
| quickUmap | run umap on PCA or other dm space |
| read.bam.tags | read bam files and extract tags from minimap2 |
| RunJD | dimension reduction and visulization functions caculate... |
| sampleBackgroundSeq | sample background sequences based on mathed GC content... |
| sampleCell | sampling background cells |
| simulateDoubletMatrix | simulate doublet matrix |
| TSSenrichment | Compute TSS enrichment score for each cell |
| TSSenrichmentPlot | plot TSSenrichment |
