Signac
Analysis of Single-Cell Chromatin Data

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30
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Signac: Analysis of Single-Cell Chromatin Data
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API

API for Signac
Analysis of Single-Cell Chromatin Data

Global functions
.onLoad Source code
AccessiblePeaks Man page Source code
AddChromatinModule Man page Source code
AddFragments Source code
AddMissing Source code
AddMotifs Man page Source code
AddMotifs.Assay Man page Source code
AddMotifs.ChromatinAssay Man page Source code
AddMotifs.Seurat Man page Source code
AddMotifs.StdAssay Man page Source code
AddMotifs.default Man page Source code
AggregateTiles Man page Source code
AggregateTiles.ChromatinAssay Man page Source code
AggregateTiles.Seurat Man page Source code
AggregateTiles.default Man page Source code
AlleleFreq Man page Source code
AlleleFreq.Assay Man page Source code
AlleleFreq.Seurat Man page Source code
AlleleFreq.StdAssay Man page Source code
AlleleFreq.default Man page Source code
Annotation Man page Source code
Annotation.ChromatinAssay Man page Source code
Annotation.Seurat Man page Source code
Annotation<- Man page
Annotation<-.ChromatinAssay Man page
Annotation<-.Seurat Man page
AnnotationPlot Man page Source code
AssignFragCellnames Source code
AverageCountMatrix Source code
AverageCounts Man page Source code
BackgroundMeanNorm Source code
BigwigTrack Man page Source code
BinarizeCounts Man page Source code
BinarizeCounts.Assay Man page Source code
BinarizeCounts.Seurat Man page Source code
BinarizeCounts.default Man page Source code
BinaryIdentMatrix Source code
CalcN Source code
CallPeaks Man page Source code
CallPeaks.ChromatinAssay Man page Source code
CallPeaks.Fragment Man page Source code
CallPeaks.Seurat Man page Source code
CallPeaks.default Man page Source code
Cells Man page
Cells.Fragment Man page Source code
Cells<- Man page
Cells<-.Fragment Man page
CellsPerGroup Man page Source code
ChromatinAssay Man page
ChromatinAssay-class Man page
ClosestFeature Man page Source code
ClusterClonotypes Man page Source code
CollapseToLongestTranscript Source code
CombineTiles Source code
CombineTracks Man page Source code
ComputeTile Source code
ComputeTotalCoverage Source code
ConnectionsToLinks Man page Source code
ConvertMotifID Man page Source code
ConvertMotifID.Assay Man page Source code
ConvertMotifID.ChromatinAssay Man page Source code
ConvertMotifID.Motif Man page Source code
ConvertMotifID.Seurat Man page Source code
ConvertMotifID.StdAssay Man page Source code
ConvertMotifID.default Man page Source code
CountFragments Man page Source code
CountsInRegion Man page Source code
CoverageBrowser Man page Source code
CoveragePlot Man page Source code
CoverageTrack Source code
CreateChromatinAssay Man page Source code
CreateFragmentObject Man page Source code
CreateMotifMatrix Man page Source code
CreateMotifObject Man page Source code
CreateTilePlot Source code
DensityScatter Man page Source code
DepthCor Man page Source code
DistanceToTSS Source code
DownsampleFeatures Man page Source code
ExpressionPlot Man page Source code
Extend Man page Source code
FRiP Man page Source code
FUN Source code
FeatureMatrix Man page Source code
FilterCells Man page Source code
FindClonotypes Man page Source code
FindExpectedInsertions Source code
FindMotifs Man page Source code
FindTopFeatures Man page Source code
FindTopFeatures.Assay Man page Source code
FindTopFeatures.Seurat Man page Source code
FindTopFeatures.StdAssay Man page Source code
FindTopFeatures.default Man page Source code
FoldChange.ChromatinAssay Source code
Footprint Man page Source code
Footprint.ChromatinAssay Man page Source code
Footprint.Seurat Man page Source code
FractionCountsInRegion Man page Source code
Fragment Man page
Fragment-class Man page
FragmentHistogram Man page Source code
Fragments Man page Source code
Fragments.ChromatinAssay Man page Source code
Fragments.Seurat Man page Source code
Fragments<- Man page
Fragments<-.ChromatinAssay Man page
Fragments<-.Seurat Man page
GRangesToString Man page Source code
GeneActivity Man page Source code
GenomeBinMatrix Man page Source code
GetAssayData.ChromatinAssay Source code
GetCellsInRegion Man page Source code
GetFootprintData Man page Source code
GetFootprintRegions Source code
GetFragmentData Man page Source code
GetGRangesFromEnsDb Man page Source code
GetIndexFile Source code
GetIntersectingFeatures Man page Source code
GetLinkedGenes Man page Source code
GetLinkedPeaks Man page Source code
GetMotifData Man page Source code
GetMotifData.ChromatinAssay Man page Source code
GetMotifData.Motif Man page Source code
GetMotifData.Seurat Man page Source code
GetMotifSize Source code
GetTSSPositions Man page Source code
IdentifyVariants Man page Source code
IdentifyVariants.Assay Man page Source code
IdentifyVariants.Seurat Man page Source code
IdentifyVariants.StdAssay Man page Source code
IdentifyVariants.default Man page Source code
InsertionBias Man page Source code
InsertionBias.ChromatinAssay Man page Source code
InsertionBias.Seurat Man page Source code
IntersectMatrix Man page Source code
Jaccard Man page Source code
LayerData.ChromatinAssay Source code
LinkPeaks Man page Source code
LinkPlot Man page Source code
Links Man page Source code
Links.ChromatinAssay Man page Source code
Links.Seurat Man page Source code
Links<- Man page
Links<-.ChromatinAssay Man page
Links<-.Seurat Man page
LinksToGRanges Source code
LookupGeneCoords Man page Source code
MatchRegionStats Man page Source code
Motif Man page
Motif-class Man page
MotifCounts Man page Source code
MotifPlot Man page Source code
Motifs Man page Source code
Motifs.ChromatinAssay Man page Source code
Motifs.Seurat Man page Source code
Motifs<- Man page
Motifs<-.ChromatinAssay Man page
Motifs<-.Seurat Man page
NonOverlapping Source code
NucleosomeSignal Man page Source code
PeakPlot Man page Source code
PlotFootprint Man page Source code
ProcessLetter Source code
ReadMGATK Man page Source code
RegionHeatmap Man page Source code
RegionMatrix Man page Source code
RegionMatrix.ChromatinAssay Man page Source code
RegionMatrix.Seurat Man page Source code
RegionMatrix.default Man page Source code
RegionPlot Man page Source code
RegionStats Man page Source code
RegionStats.ChromatinAssay Man page Source code
RegionStats.Seurat Man page Source code
RegionStats.default Man page Source code
RenameCells.ChromatinAssay Source code
RenameCells.Fragment Source code
RunChromVAR Man page Source code
RunChromVAR.ChromatinAssay Man page Source code
RunChromVAR.Seurat Man page Source code
RunFootprint Source code
RunSVD Man page Source code
RunSVD.Assay Man page Source code
RunSVD.Seurat Man page Source code
RunSVD.StdAssay Man page Source code
RunSVD.default Man page Source code
RunTFIDF Man page Source code
RunTFIDF.Assay Man page Source code
RunTFIDF.Seurat Man page Source code
RunTFIDF.StdAssay Man page Source code
RunTFIDF.default Man page Source code
SetAssayData.ChromatinAssay Source code
SetMotifData Man page Source code
SetMotifData.ChromatinAssay Man page Source code
SetMotifData.Motif Man page Source code
SetMotifData.Seurat Man page Source code
Signac Man page
Signac-package Man page
SingleCoveragePlot Source code
SingleFeatureMatrix Source code
SortIdents Man page Source code
SparseMatrixFromBaseCounts Source code
SplitFragments Man page Source code
StringToGRanges Man page Source code
SubsetMatrix Man page Source code
TSSEnrichment Man page Source code
TSSFast Source code
TSSPlot Man page Source code
TilePlot Man page Source code
UnifyPeaks Man page Source code
UpdateChromatinObject Source code
UpdatePath Man page Source code
ValidateCells Man page Source code
ValidateFragments Man page Source code
ValidateHash Man page Source code
VariantPlot Man page Source code
[.Motif Man page
as.ChromatinAssay Man page Source code
as.ChromatinAssay.Assay Man page Source code
atac_small Man page
blacklist_ce10 Man page
blacklist_ce11 Man page
blacklist_dm3 Man page
blacklist_dm6 Man page
blacklist_hg19 Man page
blacklist_hg38 Man page
blacklist_hg38_unified Man page
blacklist_mm10 Man page
corSparse Man page Source code
countOverlaps Man page
countOverlaps,ChromatinAssay,ChromatinAssay-method Man page
countOverlaps,ChromatinAssay,Vector-method Man page
countOverlaps,Seurat,Seurat-method Man page
countOverlaps,Seurat,Vector-method Man page
countOverlaps,Vector,ChromatinAssay-method Man page
countOverlaps,Vector,Seurat-method Man page
coverage Man page
coverage,ChromatinAssay-method Man page
coverage,Seurat-method Man page
dim.Motif Source code
dimnames.Motif Source code
disjoin Man page
disjoin,ChromatinAssay-method Man page
disjoin,Seurat-method Man page
disjointBins Man page
disjointBins,ChromatinAssay-method Man page
disjointBins,Seurat-method Man page
distance Man page
distance,ANY,ChromatinAssay-method Man page
distance,ANY,Seurat-method Man page
distance,ChromatinAssay,ANY-method Man page
distance,ChromatinAssay,ChromatinAssay-method Man page
distance,Seurat,ANY-method Man page
distance,Seurat,Seurat-method Man page
distanceToNearest Man page
distanceToNearest,ANY,ChromatinAssay-method Man page
distanceToNearest,ANY,Seurat-method Man page
distanceToNearest,ChromatinAssay,ANY-method Man page
distanceToNearest,ChromatinAssay,ChromatinAssay-method Man page
distanceToNearest,Seurat,ANY-method Man page
distanceToNearest,Seurat,Seurat-method Man page
extract_tss_counts Source code
filterCells Source code
findOverlaps Man page
findOverlaps,ChromatinAssay,ChromatinAssay-method Man page
findOverlaps,ChromatinAssay,Vector-method Man page
findOverlaps,Seurat,Seurat-method Man page
findOverlaps,Seurat,Vector-method Man page
findOverlaps,Vector,ChromatinAssay-method Man page
findOverlaps,Vector,Seurat-method Man page
findOverlaps-methods Man page
follow Man page
follow,ANY,ChromatinAssay-method Man page
follow,ANY,Seurat-method Man page
follow,ChromatinAssay,ANY-method Man page
follow,ChromatinAssay,ChromatinAssay-method Man page
follow,Seurat,ANY-method Man page
follow,Seurat,Seurat-method Man page
gaps Man page
gaps,ChromatinAssay-method Man page
gaps,Seurat-method Man page
genome Man page
genome,ChromatinAssay-method Man page
genome,Seurat-method Man page
genome<-,ChromatinAssay-method Man page
genome<-,Seurat-method Man page
get_density Source code
get_heatmap_data Source code
granges Man page
granges,ChromatinAssay-method Man page
granges,Seurat-method Man page
granges-methods Man page
groupCommand Source code
head.Fragment Man page Source code
inter-range-methods Man page
isCircular Man page
isCircular,ChromatinAssay-method Man page
isCircular,Seurat-method Man page
isCircular<-,ChromatinAssay-method Man page
isCircular<-,Seurat-method Man page
isDisjoint Man page
isDisjoint,ChromatinAssay-method Man page
isDisjoint,Seurat-method Man page
merge.ChromatinAssay Source code
nearest Man page
nearest,ANY,ChromatinAssay-method Man page
nearest,ANY,Seurat-method Man page
nearest,ChromatinAssay,ANY-method Man page
nearest,ChromatinAssay,ChromatinAssay-method Man page
nearest,Seurat,ANY-method Man page
nearest,Seurat,Seurat-method Man page
nearest-methods Man page
precede Man page
precede,ANY,ChromatinAssay-method Man page
precede,ANY,Seurat-method Man page
precede,ChromatinAssay,ANY-method Man page
precede,ChromatinAssay,ChromatinAssay-method Man page
precede,Seurat,ANY-method Man page
precede,Seurat,Seurat-method Man page
range Man page
range,ChromatinAssay-method Man page
range,Seurat-method Man page
record_overlapping Source code
reduce Man page
reduce,ChromatinAssay-method Man page
reduce,Seurat-method Man page
reexports Man page
reformat_annotations Source code
seqinfo Man page
seqinfo,ChromatinAssay-method Man page
seqinfo,Seurat-method Man page
seqinfo-methods Man page
seqinfo<-,ChromatinAssay-method Man page
seqinfo<-,Seurat-method Man page
seqlengths Man page
seqlengths,ChromatinAssay-method Man page
seqlengths,Seurat-method Man page
seqlengths<-,ChromatinAssay-method Man page
seqlengths<-,Seurat-method Man page
seqlevels Man page
seqlevels,ChromatinAssay-method Man page
seqlevels,Seurat-method Man page
seqlevels<-,ChromatinAssay-method Man page
seqlevels<-,Seurat-method Man page
seqnames Man page
seqnames,ChromatinAssay-method Man page
seqnames,Seurat-method Man page
seqnames<-,ChromatinAssay-method Man page
seqnames<-,Seurat-method Man page
splitFragments Source code
split_body Source code
subset.ChromatinAssay Source code
subset.Fragment Man page Source code
subset.Motif Man page Source code
theme_browser Man page Source code
validateCells Source code
Signac documentation built on Aug. 19, 2025, 1:11 a.m.

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