Signac v0.2.4

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Analysis of Single-Cell Chromatin Data

A framework for the analysis and exploration of single-cell chromatin data. The 'Signac' package contains functions for quantifying single-cell chromatin data, computing per-cell quality control metrics, dimension reduction and normalization, visualization, and DNA sequence motif analysis. Reference: Stuart and Butler et al. (2019) <doi:10.1016/j.cell.2019.05.031>.

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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")

Functions in Signac

Name Description
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
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Details

Date 2020-03-04
biocViews
License MIT + file LICENSE
Encoding UTF-8
LazyData true
RoxygenNote 7.0.2
URL https://github.com/timoast/signac, https://satijalab.org/signac
BugReports https://github.com/timoast/signac/issues
Collate 'data.R' 'generics.R' 'dimension_reduction.R' 'motifs.R' 'objects.R' 'preprocessing.R' 'utilities.R' 'visualization.R'
NeedsCompilation no
Packaged 2020-03-04 19:15:26 UTC; stuartt
Repository CRAN
Date/Publication 2020-03-13 08:50:02 UTC

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