API for Honchkrow/SignacSlim
The slim version of signac

Global functions
AddFragments	Source code
AddMetaData	Man page
AddMissingCells	Source code
AggregateTiles	Man page Source code
AlleleFreq	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
ApplyMatrixByGroup	Man page
Assay-class	Man page
Assays	Man page
AssignFragCellnames	Source code
BinarizeCounts	Man page Source code
Cells	Man page
Cells.Fragment	Man page Source code
Cells<-	Man page
Cells<-.Fragment	Man page
CellsByIdentities	Man page
ChromatinAssay	Man page
ChromatinAssay-class	Man page
ChunkGRanges	Man page Source code
CollapseToLongestTranscript	Source code
Command	Man page
CountFragments	Man page Source code
CreateAssayObject	Man page
CreateChromatinAssay	Man page Source code
CreateDimReducObject	Man page
CreateFragmentObject	Man page Source code
CreateRegionPileupMatrix	Man page
CreateSeuratObject	Man page
DefaultAssay	Man page
DefaultAssay<-	Man page
DimReduc-class	Man page
Distances	Man page
Embeddings	Man page
Extend	Man page
ExtractCell	Man page Source code
ExtractFragments	Man page Source code
FeatureMatrix	Man page Source code
FetchData	Man page
FilterCells	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
GetAssay	Man page Source code
GetAssayData	Man page
GetAssayData.ChromatinAssay	Source code
GetCellsInRegion	Man page Source code
GetFragmentData	Man page Source code Source code
GetGRangesFromEnsDb	Man page Source code
GetGroups	Man page Source code
GetImage	Man page
GetTSSPositions	Man page Source code
GetTissueCoordinates	Man page
Graph-class	Man page
HVFInfo	Man page
Idents	Man page
Idents<-	Man page
Images	Man page
Index	Man page
Index<-	Man page
Indices	Man page
IsGlobal	Man page
JS	Man page
JS<-	Man page
JackStrawData-class	Man page
Key	Man page
Key<-	Man page
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
Loadings	Man page
Loadings<-	Man page
LogSeuratCommand	Man page
Misc	Man page
Misc<-	Man page
Neighbor-class	Man page
Neighbors	Man page
NucleosomeSignal	Man page Source code
PartialMatrix	Source code
Project	Man page
Project<-	Man page
Radius	Man page
Read10X_h5	Man page Source code
Reductions	Man page
RegionMatrix	Man page Source code
RegionStats	Man page Source code
RenameCells	Man page
RenameCells.ChromatinAssay	Source code
RenameCells.Fragment	Source code
RenameIdents	Man page
ReorderIdent	Man page
RowMergeSparseMatrices	Man page
SVFInfo	Man page
SetAssayData	Man page
SetAssayData.ChromatinAssay	Source code
SetIdent	Man page
SetIfNull	Man page Source code
Seurat-class	Man page
SeuratCommand-class	Man page
SingleFeatureMatrix	Man page Source code
SpatialImage-class	Man page
SpatiallyVariableFeatures	Man page
SplitFragments	Man page Source code
StashIdent	Man page
Stdev	Man page
StringToGRanges	Man page Source code
TSSEnrichment	Man page Source code
TSSFast	Source code
TSSPlot	Man page Source code
Tool	Man page
Tool<-	Man page
UpdatePath	Man page Source code
UpdateSeuratObject	Man page
UpdateSlots	Man page Source code
ValidateCells	Man page Source code
ValidateFragments	Man page Source code
ValidateHash	Man page Source code
VariableFeatures	Man page
VariableFeatures<-	Man page
WhichCells	Man page
as.ChromatinAssay	Man page Source code
as.ChromatinAssay.Assay	Man page Source code
as.Graph	Man page
as.Neighbor	Man page
as.Seurat	Man page
as.sparse	Man page
countOverlaps	Man page
countOverlaps,ChromatinAssay,ChromatinAssay-method	Man page
countOverlaps,ChromatinAssay,Vector-method	Man page
countOverlaps,Vector,ChromatinAssay-method	Man page
coverage	Man page
coverage,ChromatinAssay-method	Man page
disjoin	Man page
disjoin,ChromatinAssay-method	Man page
disjointBins	Man page
disjointBins,ChromatinAssay-method	Man page
distance	Man page
distance,ANY,ChromatinAssay-method	Man page
distance,ChromatinAssay,ANY-method	Man page
distance,ChromatinAssay,ChromatinAssay-method	Man page
distanceToNearest	Man page
distanceToNearest,ANY,ChromatinAssay-method	Man page
distanceToNearest,ChromatinAssay,ANY-method	Man page
distanceToNearest,ChromatinAssay,ChromatinAssay-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,Vector,ChromatinAssay-method	Man page
findOverlaps-methods	Man page
follow	Man page
follow,ANY,ChromatinAssay-method	Man page
follow,ChromatinAssay,ANY-method	Man page
follow,ChromatinAssay,ChromatinAssay-method	Man page
gaps	Man page
gaps,ChromatinAssay-method	Man page
genome	Man page
genome,ChromatinAssay-method	Man page
genome<-,ChromatinAssay-method	Man page
granges	Man page
granges,ChromatinAssay-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<-,ChromatinAssay-method	Man page
isDisjoint	Man page
isDisjoint,ChromatinAssay-method	Man page
isRemote	Man page Source code
merge.ChromatinAssay	Source code
nearest	Man page
nearest,ANY,ChromatinAssay-method	Man page
nearest,ChromatinAssay,ANY-method	Man page
nearest,ChromatinAssay,ChromatinAssay-method	Man page
nearest-methods	Man page
precede	Man page
precede,ANY,ChromatinAssay-method	Man page
precede,ChromatinAssay,ANY-method	Man page
precede,ChromatinAssay,ChromatinAssay-method	Man page
range	Man page
range,ChromatinAssay-method	Man page
reduce	Man page
reduce,ChromatinAssay-method	Man page
reexports	Man page
seqinfo	Man page
seqinfo,ChromatinAssay-method	Man page
seqinfo-methods	Man page
seqinfo<-,ChromatinAssay-method	Man page
seqlengths	Man page
seqlengths,ChromatinAssay-method	Man page
seqlengths<-,ChromatinAssay-method	Man page
seqlevels	Man page
seqlevels,ChromatinAssay-method	Man page
seqlevels<-,ChromatinAssay-method	Man page
seqnames	Man page
seqnames,ChromatinAssay-method	Man page
seqnames<-,ChromatinAssay-method	Man page
splitFragments	Source code
subset.ChromatinAssay	Source code
validateCells	Source code