differential-accessibility

The differential-accessibility pipeline is designed to identify genomic regions exhibiting significant differences in chromatin accessibility between experimental conditions (e.g., treatment vs. control). It integrates DESeq2 for robust statistical testing and supports workflows starting from either BAM files (aligned ATAC-seq/DNase-seq reads) or a precomputed count matrix. Use it when you aim to identify changes in chromatin accessibility across biological conditions, treatments, or cell types. It is particularly suited for ATAC-seq, DNase-seq, or other open-chromatin profiling datasets.