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Harmonize CellNames_scseqCMs6 signatures with malignant nomenclature … - #390

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fix/harmonize-cellnames-scseqcms6-malignant
Jun 26, 2026
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Harmonize CellNames_scseqCMs6 signatures with malignant nomenclature …#390
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fix/harmonize-cellnames-scseqcms6-malignant

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@hatjek hatjek commented Jun 26, 2026

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…(#388/#389)

PRs #388/#389 harmonized the malignant annotation in CellTypes_v1.tsv, removing the melanoma/colorectal child cell types and keeping only the 'malignant cell' (short_dblabel 'Malignant') parent. The CellNames_scseqCMs6 signature datasets still referenced the removed terms, leaving besca internally inconsistent (obtain_new_label raised "Error trying to reach MelMelanoma in nomenclature").

  • Merge MelMelanoma + ColorectalCancer signatures into a single 'Malignant' signature (union of marker genes) in config + sigs, human + mouse.
  • Rename 'Microglia' -> 'Microglial' to match the existing nomenclature short_dblabel 'microglial cell' (pre-existing typo).

Every CellNames_scseqCMs6 config term / signature name now resolves to a short_dblabel in CellTypes_v1.tsv.

…388/#389)

PRs #388/#389 harmonized the malignant annotation in CellTypes_v1.tsv, removing
the melanoma/colorectal child cell types and keeping only the 'malignant cell'
(short_dblabel 'Malignant') parent. The CellNames_scseqCMs6 signature datasets
still referenced the removed terms, leaving besca internally inconsistent
(obtain_new_label raised "Error trying to reach MelMelanoma in nomenclature").

- Merge MelMelanoma + ColorectalCancer signatures into a single 'Malignant'
  signature (union of marker genes) in config + sigs, human + mouse.
- Rename 'Microglia' -> 'Microglial' to match the existing nomenclature
  short_dblabel 'microglial cell' (pre-existing typo).

Every CellNames_scseqCMs6 config term / signature name now resolves to a
short_dblabel in CellTypes_v1.tsv.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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hatjek merged commit 1655982 into main Jun 26, 2026
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hatjek deleted the fix/harmonize-cellnames-scseqcms6-malignant branch June 26, 2026 09:51
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