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Felipe da Veiga Leprevost
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Dec 6, 2022
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### Added | ||
- Added new flag `--removecontam` to the report command to remove contaminants from the reports | ||
- Added a new combined_psm report to abacus (beta) | ||
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### Changed | ||
- Updated the TMT-Integrator to match with the version v4.0.0 | ||
- Updated the pickedFDR filter | ||
- The pipeline command now accepts annotation files with prefixes | ||
- Updated PTMProphet to the latest release | ||
- Updated the database fetch with the new UniProt API (The new API is still unstable, people might experience hicups with certain cases, specially non-model organisms without reviewed sequences) | ||
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### Fixed | ||
- Contaminant tags are now added to Human sequences as well | ||
- Several minor fixes and updates | ||
- Added a fix to fix errorrs causes by division-by-zero errors (PR by @chhh) | ||
- Fixed the protein coverage calculations to take into account all peptides | ||
- Adjusted the msstats file format, added Purity to all plex sizes. |
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