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Yo Akiyama edited this page Sep 1, 2021 · 5 revisions

v0.0.8 Updates

Bug fixes
Renaming command line arg cosmic to reference
Support for the following mutational signature contexts:
- pcawg_COMPOSITE: 1536 SBS + 78 DBS + 83 ID; Compares to PCAWG Composite reference and COSMIC3 SBS reference
- pcawg_COMPOSITE96: 96 SBS + 78 DBS + 83 ID; Compares to PCAWG Composite reference (adjusted SBS portion) and COSMIC3 SBS reference
- pcawg_SBS_ID: 1536 SBS + 83 ID; Compares to PCAWG reference (without DBS portion) and COSMIC3 SBS reference
- pcawg_SBS96_ID: 96 SBS + 83 ID; Compares to PCAWG reference (adjusted SBS portion & without DBS) and COSMIC3 SBS reference
- pcawg_SBS: 1536 SBS; Compares to PCAWG reference (without DBS or ID portion) and COSMIC3 SBS reference
- polymerase_msi: 1536 SBS + 8 ID; Compares to Polymerase + MSI reference
- polymerase_msi96: 96 SBS + 8 ID; Compares to Polymerase + MSI reference (adjusted SBS portion)
Updated COSMIC3 signatures to v3.2 (Latest March 2021 version)
Supervised NMF
Cross-validation