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Version 2.2.0

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@ymd1022 ymd1022 released this 23 Jun 15:01
· 5 commits to master since this release
v2.2.0
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Learn about vigilant mode.

Highlights

  • Updated the packaged mutation-prediction models.
  • Added clustered-noise filtration for RNA-editing-like and other clustered technical-noise patterns.
  • Added separate mitochondrial and contig filtration controls.
  • Improved RNA-feature annotation and filtration handling.
  • Improved PhyloSOLID input preparation for tree building.

What's Changed

Algorithm / processing updates

  • Updated the pretrained spatial_free_model and spatial_preserved_model mutation-prediction model artifacts.
  • Added clustered-noise detection features, including AtoG_clustered_noise and other_clustered_noise.
  • Added new filtration controls:
    • LOW_ALT_SPOT_NUM
    • CONTIG
    • MITOCHONDRIA
    • CLUSTERED_NOISE(RNA_editing)
    • CLUSTERED_NOISE
  • Split the previous combined contig/mitochondrial filtration behavior into separate configurable filters.
  • Added mitochondrial mutation-list output for calls labeled with MITOCHONDRIA.
  • Improved handling of hFDR result indexing, imprinted-region annotation, RNA-editing database matching, and panel-of-normals matching.
  • Added support for steps.phylogeny.target_barcodes when preparing PhyloSOLID input matrices.
  • Fixed an edge case in spatial-feature testing when LDA projection returns an empty result.

Documentation improvements

  • Documented new filtration controls and configuration options.
  • Updated Step 7 and phylogeny documentation for the new mutation-list and target-barcode behavior.

Notes

Assets 2
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