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AddMotifObject()
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Add a Motif object to a Seurat object |
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AverageCounts()
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Average Counts |
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BinarizeCounts()
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Binarize counts |
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CellsPerGroup()
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Cells per group |
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ClosestFeature()
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Closest Feature |
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CountsInRegion()
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CountsInRegion |
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SingleCoveragePlot() CoveragePlot()
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Plot Tn5 insertion sites over a region |
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CreateMotifMatrix()
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CreateMotifMatrix |
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CreateMotifObject()
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CreateMotifObject |
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CutMatrix()
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Generate matrix of integration sites |
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DepthCor()
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Sequencing depth correlation |
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DownsampleFeatures()
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DownsampleFeatures |
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Extend()
|
Extend |
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ExtractCell()
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ExtractCell |
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FRiP()
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Calculate fraction of reads in peaks per cell |
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FeatureMatrix()
|
FeatureMatrix |
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FilterFragments()
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FilterFragments |
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FindMotifs()
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FindMotifs |
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FindTopFeatures()
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Find most frequently observed features |
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FractionCountsInRegion()
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FractionCountsInRegion |
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FragmentHistogram()
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Plot fragment length histogram |
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GRangesToString()
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GRanges to String |
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GenomeBinMatrix()
|
GenomeBinMatrix |
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GetCellsInRegion()
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GetCellsInRegion |
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GetFragments()
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GetFragments |
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GetIntersectingFeatures()
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Find interesecting regions between two objects |
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GetMotifData()
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Retrieve a motif matrix |
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GetMotifObject()
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Retrieve a Motif object |
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GetReadsInRegion()
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GetReadsInRegion |
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IntersectMatrix()
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Intersect genomic coordinates with matrix rows |
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Jaccard()
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Calculate the Jaccard index between two matrices |
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MatchRegionStats()
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Match DNA sequence characteristics |
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MergeWithRegions()
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Region-aware object merging |
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Motif-class
|
The Motif class |
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MotifPlot()
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MotifPlot |
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NucleosomeSignal()
|
NucleosomeSignal |
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RegionStats()
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Compute base composition information for genomic ranges |
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RunChromVAR()
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Run chromVAR |
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RunSVD()
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Run singular value decomposition |
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RunTFIDF()
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Compute the term-frequency inverse-document-frequency |
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SetFragments()
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Set the fragments file path for creating plots |
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SetMotifData()
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Set motif data |
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StringToGRanges()
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String to GRanges |
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SubsetMatrix()
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Subset matrix rows and columns |
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TSSEnrichment()
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Compute TSS enrichment score per cell |
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TSSPlot()
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Plot the enrichment around TSS |
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UnifyPeaks()
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Unify genomic ranges |
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atac_small
|
A small example scATAC-seq dataset |
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blacklist_ce10
|
Genomic blacklist regions for C. elegans ce10 |
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blacklist_ce11
|
Genomic blacklist regions for C. elegans ce11 |
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blacklist_dm3
|
Genomic blacklist regions for Drosophila dm3 |
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blacklist_dm6
|
Genomic blacklist regions for Drosophila dm6 |
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blacklist_hg19
|
Genomic blacklist regions for Human hg19 |
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blacklist_hg38
|
Genomic blacklist regions for Human GRCh38 |
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blacklist_mm10
|
Genomic blacklist regions for Mouse mm10 |
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subset(<Motif>) `[`(<Motif>)
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Return a subset of a Motif object |