Single-cell chromatin state analysis with Signac.
Tim StuartAvi SrivastavaShaista MadadCaleb A LareauRahul SatijaPublished in: Nature methods (2021)
The recent development of experimental methods for measuring chromatin state at single-cell resolution has created a need for computational tools capable of analyzing these datasets. Here we developed Signac, a comprehensive toolkit for the analysis of single-cell chromatin data. Signac enables an end-to-end analysis of single-cell chromatin data, including peak calling, quantification, quality control, dimension reduction, clustering, integration with single-cell gene expression datasets, DNA motif analysis and interactive visualization. Through its seamless compatibility with the Seurat package, Signac facilitates the analysis of diverse multimodal single-cell chromatin data, including datasets that co-assay DNA accessibility with gene expression, protein abundance and mitochondrial genotype. We demonstrate scaling of the Signac framework to analyze datasets containing over 700,000 cells.
Keyphrases
- single cell
- rna seq
- gene expression
- high throughput
- dna damage
- transcription factor
- genome wide
- dna methylation
- electronic health record
- single molecule
- big data
- quality control
- circulating tumor
- induced apoptosis
- signaling pathway
- microbial community
- cell death
- data analysis
- machine learning
- cell free
- endoplasmic reticulum stress
- protein protein
- pi k akt