Man pages for timoast/signac
Analysis of Single-Cell Chromatin Data

AccessiblePeaksAccessible peaks
AddChromatinModuleAdd chromatin module
AddMotifsAdd DNA sequence motif information
AggregateTilesQuantify aggregated genome tiles
AlleleFreqCompute allele frequencies per cell
AnnotationPlotPlot gene annotations
as.ChromatinAssayConvert objects to a ChromatinAssay
atac_smallA small example scATAC-seq dataset
AverageCountsAverage Counts
BigwigTrackPlot data from BigWig files
BinarizeCountsBinarize counts
blacklist_ce10Genomic blacklist regions for C. elegans ce10 (0-based)
blacklist_ce11Genomic blacklist regions for C. elegans ce11 (0-based)
blacklist_dm3Genomic blacklist regions for Drosophila dm3 (0-based)
blacklist_dm6Genomic blacklist regions for Drosophila dm6 (0-based)
blacklist_hg19Genomic blacklist regions for Human hg19 (0-based)
blacklist_hg38Genomic blacklist regions for Human GRCh38
blacklist_hg38_unifiedUnified genomic blacklist regions for Human GRCh38
blacklist_mm10Genomic blacklist regions for Mouse mm10 (0-based)
CallPeaksCall peaks
CellsSet and get cell barcode information for a 'Fragment' object
CellsPerGroupCells per group
Cells-setSet and get cell barcode information for a Fragment object
ChromatinAssay-classThe ChromatinAssay class
ClosestFeatureClosest Feature
ClusterClonotypesFind relationships between clonotypes
CombineTracksCombine genome region plots
ConnectionsToLinksCicero connections to links
ConvertMotifIDConvert between motif name and motif ID
corSparseSparse matrix correlation
CountFragmentsCount fragments
CountsInRegionCounts in region
CoverageBrowserGenome browser
coverage-ChromatinAssay-methodCoverage of a ChromatinAssay object
CoveragePlotPlot Tn5 insertion frequency over a region
CreateChromatinAssayCreate ChromatinAssay object
CreateFragmentObjectCreate a Fragment object
CreateMotifMatrixCreate motif matrix
CreateMotifObjectCreate motif object
DensityScatterScatterplot colored by point density
DepthCorPlot sequencing depth correlation
DownsampleFeaturesDownsample Features
ExpressionPlotPlot gene expression
FeatureMatrixFeature Matrix
FilterCellsFilter cells from fragment file
FindClonotypesFind clonotypes
findOverlaps-methodsFind overlapping ranges for ChromatinAssay objects
FindTopFeaturesFind most frequently observed features
FootprintTranscription factor footprinting analysis
FractionCountsInRegionFraction of counts in a genomic region
Fragment-classThe Fragment class
FragmentHistogramPlot fragment length histogram
FragmentsGet the Fragment objects
FRiPCalculate fraction of reads in peaks per cell
GeneActivityCreate gene activity matrix
GenomeBinMatrixGenome bin matrix
GetCellsInRegionGet cells in a region
GetFootprintDataGet footprinting data
GetFragmentDataGet Fragment object data
GetGRangesFromEnsDbExtract genomic ranges from EnsDb object
GetIntersectingFeaturesFind intersecting regions between two objects
GetLinkedGenesGet genes linked to peaks
GetLinkedPeaksGet peaks linked to genes
GetMotifDataRetrieve a motif matrix
GetTSSPositionsFind transcriptional start sites
granges-methodsAccess genomic ranges for ChromatinAssay objects
GRangesToStringGRanges to String
head.FragmentReturn the first rows of a fragment file
IdentifyVariantsIdentify mitochondrial variants
InsertionBiasCompute Tn5 insertion bias
inter-range-methodsInter-range transformations for ChromatinAssay objects
IntersectMatrixIntersect genomic coordinates with matrix rows
JaccardCalculate the Jaccard index between two matrices
LinkPeaksLink peaks to genes
LinkPlotPlot linked genomic elements
LinksGet or set links information
LookupGeneCoordsGet gene coordinates
MatchRegionStatsMatch DNA sequence characteristics
Motif-classThe Motif class
MotifCountsCount fragments surrounding motif sites
MotifPlotPlot DNA sequence motif
MotifsGet or set a motif information
nearest-methodsFind the nearest range neighbors for ChromatinAssay objects
PeakPlotPlot peaks in a genomic region
PlotFootprintPlot motif footprinting results
ReadMGATKRead MGATK output
reexportsObjects exported from other packages
RegionHeatmapRegion heatmap
RegionMatrixRegion enrichment analysis
RegionPlotRegion plot
RegionStatsCompute base composition information for genomic ranges
RunChromVARRun chromVAR
RunSVDRun singular value decomposition
RunTFIDFCompute the term-frequency inverse-document-frequency
seqinfo-methodsAccess and modify sequence information for ChromatinAssay...
SetMotifDataSet motif data
Signac-packageSignac: Analysis of Single-Cell Chromatin Data
SplitFragmentsSplit fragment file by cell identities
StringToGRangesString to GRanges
subset.FragmentSubset a Fragment object
SubsetMatrixSubset matrix rows and columns
subset.MotifSubset a Motif object
theme_browserGenome browser theme
TilePlotPlot integration sites per cell
TSSEnrichmentCompute TSS enrichment score per cell
TSSPlotPlot signal enrichment around TSSs
UnifyPeaksUnify genomic ranges
UpdatePathUpdate the file path for a Fragment object
ValidateCellsValidate cells present in fragment file
ValidateFragmentsValidate Fragment object
ValidateHashValidate hashes for Fragment object
VariantPlotPlot strand concordance vs. VMR
timoast/signac documentation built on April 5, 2024, 1:34 a.m.