Changelog

Changelog#

Unreleased#

Added#

  • GPU-accelerated TSS enrichment scoring with streaming Parquet support.

  • Tile matrix builder with SnapATAC2-compatible "unique" count strategy.

  • Gene activity matrix builder using paired-insertion counting.

  • GPU feature selection (ArchR-style quantile filtering).

  • Multi-sample streaming feature selection via select_features_multi.

  • Fragment filtering with Polars query engine (filter_fragments).

  • CLI: convert, metrics, filter, tile, gene, features, combine.

  • Spectral embedding (tl.spectral).

  • Peak calling, peak merging, and peak matrix construction.

  • Marker peak detection with GPU-accelerated binomial test and BH correction.

  • Motif scanning from MEME format files.

  • chromVAR deviation scoring (fully GPU-accelerated).

  • GPU-accelerated preranked GSEA (tl.gsea_motif_enrichment).

  • Mini-batch LDA via Online Variational Bayes (tl.lda, tl.MiniBatchLDA).

  • Built-in chromosome sizes for hg38, hg19, mm10, mm39.

0.1.0 — initial release#

First public version of GATAC.