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Signac

Signac is a comprehensive R package for the analysis of single-cell chromatin data.

Features

Signac is designed for the analysis of single-cell chromatin data, including scATAC-seq, single-cell targeted tagmentation methods such as scCUT&Tag and scNTT-seq, and multimodal datasets that jointly measure chromatin state alongside other modalities.

Signac currently supports the following features:

  • Calling peaks
  • Quantifying per-cell counts in different genomic regions
  • 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 datasets
  • Integration with single-cell RNA-seq datasets
  • Sequence motif enrichment analysis
  • Transcription factor footprinting analysis
  • Linking peaks to correlated genes
  • Parallelization through the future package
  • Seamless interface with Seurat, SeuratWrappers, SeuratDisk, and SeuratData functionality
  • Interoperability with Bioconductor tools

Check out the Signac vignettes page for in-depth tutorials.

Quick installation

setRepositories(ind=1:3)
install.packages("Signac")

For full installation instructions see the install page.

Getting help

If you encounter a bug or have a feature request, please open an issue.

If you would like to discuss questions related to single-cell analysis, you can open a discussion.

Roadmap

Signac runs on a quarterly release schedule. Additional releases will be scheduled in the case of urgent bug fixes. The development roadmap can be viewed on GitHub here.