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


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 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.


To use Signac first make sure Bioconductor is installed:

# Install bioconductor
if (!requireNamespace("BiocManager", quietly = TRUE))

Current release

Development version

devtools::install_github("timoast/signac", ref = "develop")

For information about installing Seurat, see the Seurat website

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


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


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