ChromSCape

ChromSCape processes single-cell epigenomic data to assist the biological interpretation of chromatin landscapes within cell populations.

Key Features:

• Single-cell epigenomics analysis: Analyzes the distribution of repressive and active histone modifications as well as chromatin accessibility landscapes from single-cell datasets.
• Quality control and preprocessing: Performs QC, preprocessing, and filtering of single-cell epigenomics data.
• Batch correction: Corrects for batch effects in single-cell epigenomics datasets.
• Dimensionality reduction and visualization: Reduces dimensions and visualizes single-cell epigenomic data.
• Clustering: Clusters cells based on their chromatin landscapes.
• Differential analysis: Identifies differential chromatin modifications between cell populations.
• Gene set enrichment analysis: Performs gene set analysis on single-cell epigenomics data.

Scientific Applications:

• Tumor microenvironment deconvolution: Deconvolves chromatin landscapes within the tumor micro-environment, identifying distinct H3K27me3 landscapes associated with cell identity and breast tumor subtype.
• Characterization of chromatin heterogeneity: Characterizes the heterogeneity of chromatin marks in complex biological systems over time at single-cell resolution.

Methodology:

ChromSCape processes aligned single-cell epigenomics data through QC, preprocessing, filtering, batch correction, dimensionality reduction, clustering, differential analysis, and gene set enrichment analysis.