atac-seq-differential-accessibility - Analyze differential chromatin accessibility across conditions
Identifies chromatin regions with differential ATAC-seq accessibility using DiffBind, csaw, DESeq2, or edgeR.
Tags
Updated: 2026-10-07Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Build region count matrices
- Choose peak or window workflows
- Normalize ATAC-seq counts
- Fit differential accessibility models
- Adjust batch and hidden variance
- Interpret log2FC and FDR
Inputs
- BAM files
- Peak files
- Peak-count matrices
- Sample metadata
- Experimental conditions
- Replicate information
- Genome information
- Normalization strategy
Outputs
- Differential accessibility regions
- Normalized count matrices
- Statistical test results
- Log2 fold changes
- FDR values
- Quality-control plots
Requirements
- R environment
- DiffBind 3.12 or later
- DESeq2 1.42 or later
- edgeR 4.0 or later
- csaw 1.36 or later
- limma 3.58 or later
- GenomicRanges 1.54 or later
- sva 3.50 or later
- RUVSeq 1.36 or later