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Added new flag --removecontam to the report command to remove contaminants from the reports
Added a new combined_psm report to abacus (beta)
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 hiccups with certain cases, especially non-model organisms without reviewed sequences)
Fixed
Contaminant tags are now added to Human sequences as well
Added a fix to fix errors causes by division-by-zero errors (PR by @chhh)
Fixed the protein coverage calculations to consider all peptides
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Added
--removecontam
to the report command to remove contaminants from the reportsChanged
Fixed
This discussion was created from the release Philosopher 4.6.0.
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