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Signac v0.2.4

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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Install

install.packages('Signac')

Monthly Downloads

5,277

Version

0.2.4

License

MIT + file LICENSE

Issues

Pull Requests

Stars

Forks

Maintainer

Tim Stuart

Last Published

March 13th, 2020

Functions in Signac (0.2.4)

FractionCountsInRegion

FractionCountsInRegion
FragmentHistogram

Plot fragment length histogram
ExtractCell

ExtractCell
GetMotifObject

Retrieve a Motif object
GetReadsInRegion

GetReadsInRegion
FRiP

Calculate fraction of reads in peaks per cell
IntersectMatrix

Intersect genomic coordinates with matrix rows
FeatureMatrix

FeatureMatrix
FilterFragments

FilterFragments
Jaccard

Calculate the Jaccard index between two matrices
DownsampleFeatures

DownsampleFeatures
Extend

Extend
GetIntersectingFeatures

Find interesecting regions between two objects
blacklist_ce11

Genomic blacklist regions for C. elegans ce11
MergeWithRegions

Region-aware object merging
MatchRegionStats

Match DNA sequence characteristics
NucleosomeSignal

NucleosomeSignal
Motif-class

The Motif class
atac_small

A small example scATAC-seq dataset
MotifPlot

MotifPlot
GetMotifData

Retrieve a motif matrix
blacklist_ce10

Genomic blacklist regions for C. elegans ce10
CreateMotifMatrix

CreateMotifMatrix
GRangesToString

GRanges to String
GenomeBinMatrix

GenomeBinMatrix
StringToGRanges

String to GRanges
blacklist_hg38

Genomic blacklist regions for Human GRCh38
RegionStats

Compute base composition information for genomic ranges
SetMotifData

Set motif data
RunTFIDF

Compute the term-frequency inverse-document-frequency
FindMotifs

FindMotifs
FindTopFeatures

Find most frequently observed features
SetFragments

Set the fragments file path for creating plots
RunSVD

Run singular value decomposition
GetFragments

GetFragments
GetCellsInRegion

GetCellsInRegion
TSSPlot

Plot the enrichment around TSS
UnifyPeaks

Unify genomic ranges
RunChromVAR

Run chromVAR
blacklist_dm3

Genomic blacklist regions for Drosophila dm3
SubsetMatrix

Subset matrix rows and columns
blacklist_mm10

Genomic blacklist regions for Mouse mm10
blacklist_dm6

Genomic blacklist regions for Drosophila dm6
blacklist_hg19

Genomic blacklist regions for Human hg19
TSSEnrichment

Compute TSS enrichment score per cell
subset.Motif

Return a subset of a Motif object
AddMotifObject

Add a Motif object to a Seurat object
CutMatrix

Generate matrix of integration sites
CountsInRegion

CountsInRegion
CellsPerGroup

Cells per group
ClosestFeature

Closest Feature
SingleCoveragePlot

Plot Tn5 insertion sites over a region
BinarizeCounts

Binarize counts
CreateMotifObject

CreateMotifObject
AverageCounts

Average Counts