differential-region-analysis
CommunityFind differential genomic regions from count data.
System Documentation
What problem does it solve?
The differential-region-analysis pipeline identifies genomic regions exhibiting significant differences in signal intensity between conditions using a count-based framework and DESeq2. It supports detection of both differential accessible regions (DARs) from open-chromatin assays and differential transcription factor (TF) binding regions from TF-centric assays. The pipeline can start from aligned BAM files or a precomputed count matrix and is suitable whenever genomic signal can be summarized as read counts per region.
Core Features & Use Cases
- Consensus peak generation across replicates to define a common feature space.
- Count-matrix construction from BAMs or peak inputs, metadata preparation, and DESeq2 differential testing.
- Visualization and export of significant regions (PCA, volcano plots, DAR bed files) for downstream interpretation.
Quick Start
Provide inputs (BAMs and peak files or a count matrix) and set your qvalue and log2fc thresholds to run the analysis.
Dependency Matrix
Required Modules
None requiredComponents
Standard package💻 Claude Code Installation
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Please help me install this Skill: Name: differential-region-analysis Download link: https://github.com/BIsnake2001/ChromSkills/archive/main.zip#differential-region-analysis Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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