iSHARC

iSHARC streamlines the analysis of single-cell Multiome data through quality control, modality integration, clustering, cell type annotation, and regulatory mechanism analysis for both individual datasets and multiple integrated samples.

Key Features:

• Modular Workflow Management: The pipeline uses a Snakemake-based workflow management system for implementation, execution, and extension.
• Flexible Parameter Customization: Analysis parameters are customized via a single configuration file.
• Comprehensive Result Access: The pipeline provides different access points to results and detailed summary reports from a single run.
• Dual Analysis Modes: iSHARC analyzes individual scMultiome datasets and integrates multiple samples.
• Modality Integration: The pipeline integrates chromatin accessibility and gene expression data from the same nucleus.

Scientific Applications:

• Cancer Heterogeneity Analysis: iSHARC reveals cellular heterogeneity in cancers through simultaneous profiling of chromatin accessibility and gene expression.
• Gene Regulatory Mechanism Analysis: The pipeline analyzes regulatory mechanisms using single-cell Multiome data.
• Cell Type Annotation: iSHARC performs cell type annotation as part of the scMultiome analysis workflow.

Methodology:

iSHARC is implemented as a Snakemake-based pipeline that processes 10x Genomics single cell Multiome data through sequential steps including quality control, modality integration, clustering, cell type annotation, and regulatory mechanism analysis.