Analysis of Single-Cell Chromatin Data (original) (raw)

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

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.