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Signac v0.2.5

Signac is an extension of Seurat for the analysis of single-cell chromatin data.

Documentation can be found at https://satijalab.org/signac/

Install

# Install Bioconductor
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install()

install.packages("Signac")

# To install the development version
install.packages("devtools")
devtools::install_github("timoast/signac", ref = "develop")

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Version

Install

install.packages('Signac')

Monthly Downloads

5,368

Version

0.2.5

License

MIT + file LICENSE

Issues

Pull Requests

Stars

Forks

Maintainer

Tim Stuart

Last Published

April 16th, 2020

Functions in Signac (0.2.5)

CountsInRegion

CountsInRegion
CellsPerGroup

Cells per group
CutMatrix

Generate matrix of integration sites
BinarizeCounts

Binarize counts
ClosestFeature

Closest Feature
CreateMotifObject

CreateMotifObject
CreateMotifMatrix

CreateMotifMatrix
SingleCoveragePlot

Plot Tn5 insertion sites over a region
AddMotifObject

Add a Motif object to a Seurat object
FindTopFeatures

Find most frequently observed features
AverageCounts

Average Counts
GenomeBinMatrix

GenomeBinMatrix
FeatureMatrix

FeatureMatrix
GetMotifObject

Retrieve a Motif object
FRiP

Calculate fraction of reads in peaks per cell
MergeWithRegions

Region-aware object merging
GetCellsInRegion

GetCellsInRegion
FractionCountsInRegion

FractionCountsInRegion
GetMotifData

Retrieve a motif matrix
Motif-class

The Motif class
FilterFragments

FilterFragments
DepthCor

Sequencing depth correlation
Extend

Extend
GetReadsInRegion

GetReadsInRegion
FindMotifs

FindMotifs
IntersectMatrix

Intersect genomic coordinates with matrix rows
StringToGRanges

String to GRanges
SubsetMatrix

Subset matrix rows and columns
Jaccard

Calculate the Jaccard index between two matrices
GetIntersectingFeatures

Find interesecting regions between two objects
GetFragments

GetFragments
DownsampleFeatures

DownsampleFeatures
UnifyPeaks

Unify genomic ranges
RegionStats

Compute base composition information for genomic ranges
RunChromVAR

Run chromVAR
atac_small

A small example scATAC-seq dataset
MotifPlot

MotifPlot
MatchRegionStats

Match DNA sequence characteristics
blacklist_ce10

Genomic blacklist regions for C. elegans ce10
blacklist_dm3

Genomic blacklist regions for Drosophila dm3
SetMotifData

Set motif data
NucleosomeSignal

NucleosomeSignal
subset.Motif

Return a subset of a Motif object
SetFragments

Set the fragments file path for creating plots
blacklist_dm6

Genomic blacklist regions for Drosophila dm6
ExtractCell

ExtractCell
blacklist_ce11

Genomic blacklist regions for C. elegans ce11
blacklist_hg38

Genomic blacklist regions for Human GRCh38
FragmentHistogram

Plot fragment length histogram
TSSEnrichment

Compute TSS enrichment score per cell
blacklist_hg19

Genomic blacklist regions for Human hg19
RunSVD

Run singular value decomposition
RunTFIDF

Compute the term-frequency inverse-document-frequency
GRangesToString

GRanges to String
TSSPlot

Plot the enrichment around TSS
blacklist_mm10

Genomic blacklist regions for Mouse mm10