diff --git a/CHANGELOG.md b/CHANGELOG.md index 1961861..47f3622 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,7 @@ ## ASPEN development version +## 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consolidate scattered spike-in "when should I use this" guidance into a single decision-tree callout, and remove the outdated, unreferenced `docs/extra.md` page whose content is now covered by `docs/outputs.md`.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) diff --git a/CITATION.cff b/CITATION.cff index f8b6a85..263338a 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -29,5 +29,5 @@ identifiers: type: doi value: 10.5281/zenodo.13755867 doi: 10.5281/zenodo.13755867 -version: v1.1.2 -date-released: "2025-07-17" +version: v1.3.0 +date-released: "2026-09-17" diff --git a/VERSION b/VERSION index 0c64b5c..b6bb93f 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -1.2.0-dev +1.3.0-dev