Signac is an extension of Seurat for the analysis, interpretation, and exploration of single-cell chromatin datasets.

Features

Signac is currently focused on the analysis of single-cell ATAC-seq data, but new features will be added as experimental methods for measuring other chromatin-based modalities at single-cell resolution become more widespread. Signac is under active development, and the software supports the following features:

  • Calculating single-cell QC metrics
  • Dimensional reduction, visualization, and clustering
  • Identifying cell type-specific peaks
  • Visualizing ‘pseudo-bulk’ coverage tracks
  • Integration of multiple single-cell ATAC-seq datasets
  • Integration with single-cell RNA-seq datasets
  • Motif enrichment analysis

Please see the Signac vignettes page for examples.

Installation

To use Signac first make sure Bioconductor is installed:

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

# Tell R to also check bioconductor when installing dependencies
setRepositories(ind=1:2)

Next install Signac using devtools:

install.packages("devtools")
devtools::install_github("timoast/signac")

For information about installing Seurat, see the Seurat website

It can also be useful (but not essential) to install species-specific packages from bioconductor:

Human

BiocManager::install(c('BSgenome.Hsapiens.UCSC.hg19', 'EnsDb.Hsapiens.v75'))

Mouse

BiocManager::install(c('BSgenome.Mmusculus.UCSC.mm10', 'EnsDb.Mmusculus.v79'))