Signac is a comprehensive R package for the analysis of single-cell chromatin data.
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
Please see the Signac vignettes page for examples.
For installation instructions see the install page.