TIMS²Rescore #142
TIMS²Rescore #142
Commits on Nov 22, 2023
Commits on Dec 5, 2023
Commits on Dec 8, 2023
Commits on Jan 2, 2024
Commits on Jan 10, 2024
Commits on Jan 17, 2024
Commits on Jan 22, 2024
Commits on Jan 26, 2024
Commits on Jan 31, 2024
-
-
-
-
-
-
-
Merge branch 'timsRescore' of https://github.com/rodvrees/ms2rescore …
…into timsRescore
-
-
-
-
-
-
Commits on Feb 2, 2024
Commits on Feb 17, 2024
Commits on Feb 18, 2024
Commits on Feb 20, 2024
Commits on Feb 21, 2024
-
-
Add IM2Deep feature generator (#121)
* im2deep * models + debug * fix * add models * fixes in im2deep.py * fixes in im2deep.py * im2deep implementation * CCS shift calculation fix * models + plot * add unused argument * IM2Deep plot correct labels * calibrate per charge option * new models and reference * correct format reference * fix model name in IM2Deep * change use of reference dataset * IM2Deep calibrate correctly * Implement IM2Deep package * GUI changes im2deep * add im2deep to pyproject * change dockerfile * optimise spectrum parsing * update toml file * added debug logging * requested changes * change numpy version upper limit * fix bug * Use newer setup-python action; revert numpy upper limit * Fix numpy version for py311 * Update pyproject.toml Use semi-colon instead of comma's in dependencies * requested changes * Update ms2rescore/feature_generators/im2deep.py --------- Co-authored-by: rodvrees <[email protected]> Co-authored-by: rodvrees <[email protected]> Co-authored-by: rodvrees <[email protected]> Co-authored-by: RalfG <[email protected]>
5 people authoredFeb 21, 2024
Commits on Feb 22, 2024
-
Merge branch 'timsRescore' of https://github.com/compomics/ms2rescore …
…into timsRescore
-
Commits on Feb 28, 2024
Commits on Mar 25, 2024
Commits on Mar 28, 2024
-
MS2PIPFeatureGenerator: Ensure spectrum path is string (temp fix for …
…timsrust_pyo3, until fixed in ms2pip).
Commits on Mar 29, 2024
Commits on Apr 5, 2024
Commits on Apr 8, 2024
Commits on Apr 9, 2024
-
Merge branch 'main' of https://github.com/compomics/ms2rescore into p…
…eptide-num-fix
-
Add new tims2rescore entrypoint with tims-specific config defaults; u…
…pdate and sort dependencies
-
-
-
-
-
-
-
Merge branch 'timsRescore' of https://github.com/compomics/ms2rescore …
…into peptide-num-fix
-
Merge branch 'timsRescore' of https://github.com/compomics/ms2rescore …
…into peptide-num-fix
-
Commits on Apr 10, 2024
-
-
-
-
Apply suggestions from code review ♻️
♻️ Co-authored-by: Ralf Gabriels <[email protected]>
-
-
Merge pull request #144 from compomics/peptide-num-fix
Fixes for MS²Rescore report
-
Commits on Apr 12, 2024
Commits on Apr 14, 2024
Commits on Apr 17, 2024
Commits on Apr 19, 2024
Commits on Apr 25, 2024
Commits on May 2, 2024
Commits on Jul 4, 2024
-
- Add option to pass train_fdr to mokapot; Changed: - Split functions to add mokapot confidence - Implement workaround for broken PEP calculation if best PSM is decoy - Still write PSMs to file, even if rescoring step failed. Still skip report generation
-
Split removing invalid AAs from reading PSM files step. Now also work…
…s when passed an in-memory PSMList.
-
-
-
Commits on Jul 8, 2024
-
Add options
max_psm_rank_inputandmax_psm_rank_outputto control…… multi-rank rescoring.
-
-
only install binary distributions
I'm not sure why during the resolve, pip tries sckit-learn 1.1.2, and that requires a build, which fails. The same thing happens using `pip install --ignore-installed --dry-run .`. But generally, it probably makes sense to avoid compiling from source in a github action.
Commits on Jul 9, 2024
-
Explicitly pass scores to 'assign_confidence' to avoid 'no psms under…
… eval_fdr' error when calculating q-values and PEPs.
-