Auto irt#5

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jcharkow wants to merge 611 commits intodevelopfrom

This pull request is big! We're only showing the most recent 250 commits

Commits on Feb 1, 2023

FAIMS support and quant in FFID

timosachsenberg
authored and
timosachsenberg
committed

Commits on Feb 9, 2023

Merge remote-tracking branch 'origin/develop' into feature/NuXL

timosachsenberg
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timosachsenberg
committed
add timsTOF IM support

timosachsenberg
authored and
timosachsenberg
committed

Commits on Feb 10, 2023

Commits on Feb 13, 2023

Merge remote-tracking branch 'origin/feature_SVR' into feature/NuXL

timosachsenberg
authored and
timosachsenberg
committed

Commits on Feb 14, 2023

inital support for RT prediction

timosachsenberg
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timosachsenberg
committed

Commits on Feb 15, 2023

RT prediction of XLed peptides

timosachsenberg
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timosachsenberg
committed

Commits on Feb 16, 2023

update SimpleSVM

timosachsenberg
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timosachsenberg
committed

Commits on Feb 21, 2023

expand SVR

timosachsenberg
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timosachsenberg
committed
finished simple SVR

timosachsenberg
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timosachsenberg
committed

Commits on Mar 16, 2023

also annotate ions for non-cross-linked peptides

timosachsenberg
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timosachsenberg
committed

Commits on Mar 17, 2023

moved annotation and location of linear peptides into function

timosachsenberg
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timosachsenberg
committed

Commits on Apr 19, 2023

Merge remote-tracking branch 'origin/develop' into feature/NuXL

timosachsenberg
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timosachsenberg
committed
merge to develop fixes

timosachsenberg
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timosachsenberg
committed

Commits on Apr 25, 2023

fixed order bug (doesn't change results)

timosachsenberg
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timosachsenberg
committed

Commits on Apr 26, 2023

good, relatively small feature set for svm based rescoring

timosachsenberg
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timosachsenberg
committed

Commits on May 10, 2023

add DNA BrU preset

timosachsenberg
authored and
timosachsenberg
committed

Commits on May 23, 2023

some safeguard for empty spectra after precursor filtering

timosachsenberg
authored and
timosachsenberg
committed

Commits on Jul 12, 2023

Merge remote-tracking branch 'origin/develop' into feature/NuXL

timosachsenberg
authored and
timosachsenberg
committed

Commits on Aug 8, 2023

Merge remote-tracking branch 'origin/develop' into feature/NuXL

timosachsenberg
authored and
timosachsenberg
committed

Commits on Aug 10, 2023

Merge remote-tracking branch 'origin/develop' into feature/NuXL

timosachsenberg
authored and
timosachsenberg
committed
merge

timosachsenberg
authored and
timosachsenberg
committed

Commits on Aug 11, 2023

add sequence level q-value to protein report

timosachsenberg
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timosachsenberg
committed

Commits on Oct 17, 2023

Merge remote-tracking branch 'origin/develop' into feature/NuXL

timosachsenberg
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timosachsenberg
committed

Commits on Oct 18, 2023

Update executables.cmake
timosachsenberg
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add nuxl

timosachsenberg
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timosachsenberg
committed
Update executables.cmake
Arslan-Siraj
authored
sort executables by name
timosachsenberg
authored
Merge pull request #7141 from Arslan-Siraj/feature/NuXL
timosachsenberg
authored

Commits on Nov 14, 2023

Merge remote-tracking branch 'origin/develop' into feature/NuXL

timosachsenberg
authored and
timosachsenberg
committed
update executables

timosachsenberg
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timosachsenberg
committed
update branch

timosachsenberg
authored and
timosachsenberg
committed

Commits on Nov 29, 2023

Merge remote-tracking branch 'origin/develop' into feature/NuXL

timosachsenberg
authored and
timosachsenberg
committed

Commits on Nov 30, 2023

Merge remote-tracking branch 'origin/develop' into feature/NuXL

timosachsenberg
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timosachsenberg
committed

Commits on Dec 5, 2023

update license text

timosachsenberg
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timosachsenberg
committed

Commits on Feb 8, 2024

Merge pull request #7343 from OpenMS/develop
timosachsenberg
authored

Commits on Nov 25, 2024

add NM + H2O
timosachsenberg
authored

Commits on Nov 26, 2024

fix preset

timosachsenberg
authored and
timosachsenberg
committed

Commits on Jan 22, 2025

Commits on Jan 24, 2025

add tests and documentation for deterministic fragment adduct generation
timosachsenberg
committed

Commits on Jan 31, 2025

Merge branch 'develop' into feature/NuXL
timosachsenberg
authored

Commits on Feb 25, 2025

Add support for custom RNA/DNA presets in json file (#7856)
timosachsenberg
authored

Commits on Mar 13, 2025

Commits on Apr 17, 2025

first steps of auto IRT refinement: add way to subsample the library
jcharkow
committed

Commits on Apr 18, 2025

feature: add automatic linear calibration
jcharkow
committed

Commits on May 5, 2025

Commits on May 8, 2025

Commits on May 9, 2025

Commits on May 12, 2025

Commits on May 13, 2025

refactor: peptide id - move rank to metavalue (#7997)
timosachsenberg
authored

Commits on May 14, 2025

Show file load/store progress in all TOPP tools (#8041)
cbielow
authored

Commits on May 16, 2025

Commits on May 17, 2025

fix: r^2 is zero (#8052)
jcharkow
authored

Commits on May 20, 2025

Commits on May 21, 2025

refactor: Store IDs outside of spectra. (#7974)

authored

Commits on May 22, 2025

Commits on May 23, 2025

Commits on May 30, 2025

Commits on Jun 4, 2025

Fix: correct marker ion deduplication by using 'equal_by_mass' comparator
yumengyann
committed

Commits on Jun 6, 2025

fix cmake

Martin Lang
authored and
Martin Lang
committed

Commits on Jun 7, 2025

merge deveop

Martin Lang
authored and
Martin Lang
committed
add constructor

Martin Lang
authored and
Martin Lang
committed
fix bug

Martin Lang
authored and
Martin Lang
committed
fx counting if openmp disabled

Martin Lang
authored and
Martin Lang
committed

Commits on Jun 8, 2025

fix test
timosachsenberg
committed

Commits on Jun 22, 2025

OpenSwath: add parameter to adjust non linear irt retention time extraction window (#8084)
jcharkow
authored

Commits on Jun 23, 2025

Commits on Jun 25, 2025

Commits on Jun 26, 2025

convert hmtl table to markdown (#8092)
timosachsenberg
authored

Commits on Jun 30, 2025

Better peptide table in protein_quantifier output (#8094)
timosachsenberg
authored

Commits on Jul 1, 2025

Commits on Jul 4, 2025

[GITHUB]: Add issue templates with forms
pjones
committed

Commits on Jul 7, 2025

Arrow Integration + Test in CI (#8091)
Avni2000
authored

Commits on Jul 8, 2025

Commits on Jul 10, 2025

Commits on Jul 11, 2025

Commits on Jul 13, 2025

Commits on Jul 14, 2025

Commits on Jul 16, 2025

Commits on Jul 17, 2025

Commits on Jul 18, 2025

Updated/added authors section to some files
Jeremi Maciejewski
committed
Merge branch 'develop' of github.com:OpenMS/OpenMS into Semi-specific_digestion
Jeremi Maciejewski
committed
Update CHANGELOG.
Jeremi Maciejewski
committed
[TEST]: Run pyOpenMS tests on Ubuntu
pjones
committed
Applied suggestions from PR review (#8130).
Jeremi Maciejewski
committed
Merge branch 'develop' of github.com:OpenMS/OpenMS into Semi-specific_digestion
Jeremi Maciejewski
committed

Commits on Jul 19, 2025

Commits on Jul 20, 2025

disable on windows (#8131)
timosachsenberg
authored

Commits on Jul 21, 2025

Added missing import to PyOpenMS test;
Jeremi Maciejewski
committed
Merge branch 'develop' of github.com:OpenMS/OpenMS into Semi-specific_digestion
Jeremi Maciejewski
committed
Typos; Code readability and correcting unrecommended use of boolean comparisons in tests.
Jeremi Maciejewski
committed
`test_ProteaseDigestion.py`: corrected minor error, use Python's operator `not` for negation.
Jeremi Maciejewski
committed
CHANGELOG wording; check whether input is sorted in semiSpecificDigestion_; missing documentation; additional tests; fix pyOpenMS tests
Jeremi Maciejewski
committed
Fix failing pyOpenMS test.
Jeremi Maciejewski
committed

Commits on Jul 22, 2025

Merge pull request #8130 from Jeremi-Maciejewski/Semi-specific_digestion
cbielow
authored

Commits on Jul 28, 2025

Tweaks for FileInfo on FASTA files (#8135)
cbielow
authored

Commits on Jul 31, 2025

grab thirdparty exes recursively rather than HARDCODING THEM
poshul
committed

Commits on Aug 1, 2025

Commits on Aug 3, 2025

Update MassTraceDetection.cpp (#8148)
timosachsenberg
authored

Commits on Aug 4, 2025