ASPEN 1.3.0

• Generate Tn5 nicking-site and read counts matrices, and the corresponding DiffATAC/DESeq2 results, from both dedup.bam (PCR/optical duplicates removed) and filtered.bam (duplicates retained, labeled nondedup), written to separate dedup/nondedup output subfolders under visualization/ and peaks/{peakcaller}/{fixed_width/counts,DiffATAC}/; previously only the duplicate-retaining filtered.bam was used. dedup is recommended for standard differential accessibility testing. (#138, @kopardev)
• Fail fast with a clear, actionable error message when a replicate has 0 reads aligned to the spike-in genome, instead of crashing with an opaque ZeroDivisionError in _compute_downsampling_scaling_factors.py; the error is now also captured in a dedicated results/spikein/compute_scaling_factors.log. (#139, @kopardev)
• Overhaul documentation for accuracy and clarity across docs/overview.md, docs/outputs.md, docs/introduction.md, docs/deployment.md, and docs/index.md: fix stale claims left over from the dedup/nondedup change, clarify how consensus peaks and ROIs are generated, add ENCODE-referenced QC rule-of-thumb callouts (library complexity, TSS enrichment, FRiP), consolidate scattered spike-in "when should I use this" guidance into a single decision-tree callout, and remove the outdated, unreferenced docs/extra.md page whose content is now covered by docs/outputs.md. (#138, @kopardev)