Ecosyste.ms: OpenCollective

An open API service for software projects hosted on Open Collective.

github.com/OpenMS/OpenMS

The codebase of the OpenMS project
https://github.com/OpenMS/OpenMS

Update DecoyGenerator.cpp

5a134700eab5fecd6a68f358742afac2d72689f4 authored over 4 years ago by Timo Sachsenberg <[email protected]>
Update DecoyGenerator.cpp

e3c63e297541c595539a685a38f3a82c35cbf0de authored over 4 years ago by Timo Sachsenberg <[email protected]>
[FEATURE] adds initial untested support for resolving the graph DURING inference.

c98950ed48897ebe61698fec0a38327a84dc9002 authored over 4 years ago by Julianus Pfeuffer <[email protected]>
[FIX] updated MapAligernIdentification to recent changes in class 'IdentificationData'

5962a66e417081f867980c08195c21e87a7c5254 authored over 4 years ago by Hendrik Weisser <[email protected]>
[INTERNAL] added some includes for completeness

914b4689f84d3543f64c61b23306cd72f769f7d3 authored over 4 years ago by Hendrik Weisser <[email protected]>
Merge branch 'mapalignerident-idfile' of https://github.com/hendrikweisser/OpenMS into idfile-integration

1e86bcc1c4b07c1e0343cf132a9e1f558ebe579f authored over 4 years ago by Hendrik Weisser <[email protected]>
Merge branch 'id-file-format' of https://github.com/hendrikweisser/OpenMS into idfile-integration

05036339a4d3b7234546118cc86f5a49c63cbce0 authored over 4 years ago by Hendrik Weisser <[email protected]>
[PXD] add python bindings

5ca4e0df2ffdb645a12e4fa730d65e8369c17c53 authored over 4 years ago by Timo Sachsenberg <[email protected]>
added test for SimpleSVM

b54c6031e6629adf9f0a1c65a14e9f010837478d authored over 4 years ago by Timo Sachsenberg <[email protected]>
[FIX] Fixes important unchecked map lookup when writing IdXML files.

Additionally prevents PercolatorAdapter from running on unsupported IdXMLs with multiple runs.

b9ebd0b98236951203a0dcfd64d2e13a5fb5ac96 authored over 4 years ago by Julianus Pfeuffer <[email protected]>
expose scaling parameters in SimpleSVM and add decoy generation in SSE

b9a6ebb32aa945a3c919724e5adb7d343e79eefd authored over 4 years ago by Timo Sachsenberg <[email protected]>
[FEATURE] Python detection and module inquiry

fd88fbfbff151a4e50646da7aac3128d59088caf authored over 4 years ago by Chris Bielow <[email protected]>
[TEST] add PythonInfo test

3c79347ebbbaddd79c951d65c72d844fbbee28e7 authored over 4 years ago by Chris Bielow <[email protected]>
Merge pull request #4582 from jpfeuffer/feature/refactorQC

[Feature] Refactor QualityControl tool

9936c2ba9ed6ab9c8ac9d3a1bd06e1b614ab10fb authored over 4 years ago by Timo Sachsenberg <[email protected]>
Write the huge CC to file.

21747878e30b44113274d084c629cac8fc216c99 authored over 4 years ago by Julianus Pfeuffer <[email protected]>
Forgot to remove DLLAPI in templated functions

2d1c419bbf7f956823419387b84cf164fb6182b8 authored over 4 years ago by Julianus Pfeuffer <[email protected]>
More smaller fixes

7c2e241afe6c63c9c49ed91539cfcc7bbb352639 authored over 4 years ago by Julianus Pfeuffer <[email protected]>
Address review comments.

612cb8dd96b7c95d6ab78fe676c7ce8c5a783769 authored over 4 years ago by Julianus Pfeuffer <[email protected]>
Merge pull request #4584 from OpenMS/feature/globalVisPreset

Added global visibility hidden preset, to silence warnings on macos. …

e30c5d2896c580348922034b388904e86ce51688 authored over 4 years ago by jpfeuffer <[email protected]>
Merge pull request #4588 from cbielow/qc_fix

Qc fix

98e28a9470377e53f278f63918663f567baa2ff5 authored over 4 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #4541 from bernt-matthias/topic/spectrast-pep.xml-ext

SpectraSTAdapter: remove apparently redundant extension

03ef216e8044118fb4491c924cbce84335c1be94 authored over 4 years ago by Timo Sachsenberg <[email protected]>
less error-prone PEP/PSM mapping in mzTab

7e17f36e48b5f398ec7c2f4dc7d62fdad023e228 authored over 4 years ago by Chris Bielow <[email protected]>
clean imports. fix test

6a5c7407e8cdb80e05a5dbd6b97eca76cb06d19a authored over 4 years ago by Julianus Pfeuffer <[email protected]>
forgot some cmake files to upgrade version (otherwise you get thousands of policy warnings)

c4df996cec8e060d7407542134765a73d931fd02 authored over 4 years ago by Builder <[email protected]>
Added global visibility hidden preset, to silence warnings on macos. Before just libraries were built with hidden.

bba89391b8588a9210d15b3f5e2a201daf5f7d32 authored over 4 years ago by Builder <[email protected]>
clean imports

b90bccf3162e0d6cbd5b88d0bbfb1259e1a4ebd4 authored over 4 years ago by Julianus Pfeuffer <[email protected]>
A little more refactor. Added TODOs to ProteomicsLFQ

6777f5419c554f3296b5343ff4f04930cae6efa3 authored over 4 years ago by Julianus Pfeuffer <[email protected]>
size policy fixed

f0522fd22a46a7bba3ed2bfe31c2104c81c30cf6 authored over 4 years ago by Chris Bielow <[email protected]>
Refactor QualityControl tool to be more useable from the library.

049d73f2c0442f9479c96ad80fac9ccc7239448d authored over 4 years ago by Julianus Pfeuffer <[email protected]>
Merge pull request #4578 from hendrikweisser/ffid-slim-label

Support for SLIM-labeling in FeatureFinderIdentification

e26c2ced530423f0c3fcfa077e38d41da1cb12dd authored over 4 years ago by jpfeuffer <[email protected]>
functional python selector

9b2e69246a6ea86aff5fffd4e916ffdc25437e7e authored over 4 years ago by Chris Bielow <[email protected]>
[DOC] clearer output message in FFid

cab03ee22ded73ddd275572db97a388962ad58ae authored over 4 years ago by Timo Sachsenberg <[email protected]>
Little fix and add scheduler type selection

adbf272849e84961c77f548acfa5badee3ef56ec authored over 4 years ago by Julianus Pfeuffer <[email protected]>
a first dummy application

a76d94e93c898998ff67a2e271e40b5238ba7500 authored over 4 years ago by Chris Bielow <[email protected]>
Merge pull request #4576 from timosachsenberg/develop

merge release 2.5 changes back to develop

c6348e527cd58d7bad637fe8849deae4ca7a2ed2 authored over 4 years ago by Timo Sachsenberg <[email protected]>
[TEST] updated test file for FeatureFinderMetaboIdent (new 'width' meta value)

7681840659411adb41e1e24382826af21c1b6bc4 authored over 4 years ago by Hendrik Weisser <[email protected]>
Merge branch 'develop' of https://github.com/OpenMS/OpenMS into swath_wizard

fbf7404e7ecce17d71cffd647de173ed09b35b78 authored over 4 years ago by Chris Bielow <[email protected]>
add wizard (empty)

366e969a9e02c019b1eebdd75b585b143a96f6ee authored over 4 years ago by Chris Bielow <[email protected]>
add python info class

e3e5e72893739bd8beb21c4a6fe662555a4549bf authored over 4 years ago by Chris Bielow <[email protected]>
fix cmake include

c234b364c1c34c0410f10cd618867ab6c274bc9f authored over 4 years ago by Chris Bielow <[email protected]>
[TEST] updated test file for FeatureFinderIdentification (new 'width' meta value)

7940a5a048b7a0a07822e395031e6c637c2a296e authored over 4 years ago by Hendrik Weisser <[email protected]>
Merge remote-tracking branch 'upstream/release/2.5.0' into develop

e66559bd24b0cc35cf6b2bfc0d10495348c6fa0c authored over 4 years ago by timosachsenberg <[email protected]>
[DOC] clarified documentation of some ElutionModelFitter parameters

33e55594da60dc6cbadd2783bda47d526ce34b21 authored over 4 years ago by Hendrik Weisser <[email protected]>
[COMMENT] small spelling fix

6320d255e36c56d9a560284b62d63f0ce604e63f authored over 4 years ago by Hendrik Weisser <[email protected]>
Merge branch 'develop' of https://github.com/OpenMS/OpenMS into ffid-slim-label

83583943619f4df008ba40ed722e538dc986c233 authored over 4 years ago by Hendrik Weisser <[email protected]>
Merge pull request #4574 from OpenMS/release-fix

pyOpenMS Release fix

d0edb434da2a9aec865c24fe33afe5aa35f1fbf9 authored over 4 years ago by Timo Sachsenberg <[email protected]>
use variable instead of member to avoid race conditions

5f73ff9e83d38f173c4556f557438848c7938997 authored over 4 years ago by Julianus Pfeuffer <[email protected]>
use endl to flush

a9bef767599c284ebea314dc4735051955a9c266 authored over 4 years ago by Julianus Pfeuffer <[email protected]>
rearrange debug

10ff4d7f5b9f344a86ce02bc2ec00466c4a8a861 authored over 4 years ago by Julianus Pfeuffer <[email protected]>
more debug out on nr edges

fc2e2a9392298194d9accb4dcdc35cdf42532b61 authored over 4 years ago by Julianus Pfeuffer <[email protected]>
Merge pull request #4573 from OpenMS/fix/textexporter

Update TextExporter.cpp

d714e49b7787ce40182ba0c185660f3a71c89f9e authored over 4 years ago by Timo Sachsenberg <[email protected]>
[BUILD] fix pyOpenMS 2.5 Release

a238a752b0f7aede483cadbe8af88d0d49047c67 authored over 4 years ago by Hannes Roest <[email protected]>
make output mandatory

88bd51fc79aeee63d75f576997391a4726a817d9 authored over 4 years ago by Timo Sachsenberg <[email protected]>
Added some debugging logs and smaller style/speed improvements.

11bf0076fc95945ca1430d116839a99d8ace45ca authored over 4 years ago by Julianus Pfeuffer <[email protected]>
Update TextExporter.cpp

fb675029ebb275a2fbf6a8c9b1a8b40bac7eddf1 authored over 4 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #4569 from bernt-matthias/topic/phosphoscoring_out

PhosphoScoring: set format for out parameter

383d7decf208bc134d9d277b72efbe134cbb40a0 authored over 4 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #4566 from jamesETsmith/add_elements

Adding isotopic abundances for several elements

6c2cfdc3d2347d4f1fd8c35027f11e3732c4168f authored over 4 years ago by Timo Sachsenberg <[email protected]>
PhosphoScoring: set format for out parameter

https://github.com/OpenMS/OpenMS/issues/4406

b232304670ed89382a884ca5181619d2c477d086 authored over 4 years ago by M Bernt <[email protected]>
Merge pull request #4568 from bernt-matthias/topic/rm-unused-test-inis

remove unused test data

d9ab0c490752e7eddadaa1edec3c79469030d410 authored over 4 years ago by Timo Sachsenberg <[email protected]>
remove unused test data

433f38bfa9cb0abadc8e2d6316480f6cf2e52434 authored over 4 years ago by M Bernt <[email protected]>
One-off errors

d5fbfa07ddde1434f9664d38c849d2f33c150037 authored over 4 years ago by jpfeuffer <[email protected]>
Adding isotopic abundances for several elements.

003543d282cc8c2031d1d0f081527f8bd096fec9 authored over 4 years ago by jamesETsmith <[email protected]>
Merge pull request #4565 from OpenMS/fix/ElutionPeakDetection

[FIX] prevent filtering of very sharp peaks

84b139899b37bdf62cce6fe603ec7eaac08ef005 authored over 4 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #4559 from timosachsenberg/feature/plfq_fixes

some minor command line cleanup of plfq and associated tools

7f4f3c76c49e14c495702cab152ba87495b44cf8 authored over 4 years ago by Timo Sachsenberg <[email protected]>
[FIX] prevent filtering of very sharp peaks

a58e0987a3a9c015618e94949de893df36e57ecd authored over 4 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #4564 from hroest/feature/doc_fixes

[DOC] documentation

4029f327e227ad1301b655579b5e7e7c5b7258ea authored over 4 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #4533 from bernt-matthias/topic/RTEval-outformat

RTEvaluation: fix output formats

ecf811ea8eb3d5bfdababcc02979642d8f1469ec authored over 4 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #4549 from OpenMS/timosachsenberg-patch-1

change default number of reported hits per spectrum in comet to 1

963b3da3946d97ddd59f299ca1d5328ad96c8160 authored over 4 years ago by Timo Sachsenberg <[email protected]>
address reviewer comments

9ce37bfb863d1c4b3d54d29c591dc99e5d3a8e92 authored over 4 years ago by Timo Sachsenberg <[email protected]>
Update ModificationsDB.h

74718ae2a2bbb81a629eed7a769af025176a20f5 authored over 4 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #4561 from OpenMS/fix/doc

[DOC] some minor fixes

39b8d8d17b71a98f1b8ab5d9c3d7fc998d4a92a6 authored over 4 years ago by Timo Sachsenberg <[email protected]>
[DOC] documentation

- add docu
- small fixes
- rename functions

aee624b17b54d8481dfda2aaf4d2c9e7d23a78ae authored over 4 years ago by Hannes Roest <[email protected]>
[DOC] some minor fixes

e5e0612dd08f3926bc2accbb19ee3ed9c33cc2b1 authored over 4 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #4560 from OpenMS/fix/doc

[Fix] doc

15903bdf8d787ed776b2f983a56c1f84029f5ba1 authored over 4 years ago by Timo Sachsenberg <[email protected]>
[NOP] some cmments

338a1efed0136cad8ce7ceaf3d505febd9e4f326 authored over 4 years ago by Timo Sachsenberg <[email protected]>
Deactivate dynamic menus for browser w/o JS

2ec9d86a0cbf274eab4651d0afff2b49e2ec4ce1 authored over 4 years ago by jpfeuffer <[email protected]>
Update CMakeLists.txt

2796a69776f29a2979008e72c633621ec9cfff41 authored over 4 years ago by jpfeuffer <[email protected]>
exclude looper

e78695f684e888bd446abb8f7bdd1ac8baf5cc72 authored over 4 years ago by jpfeuffer <[email protected]>
Update FeatureFinderIdentificationAlgorithm.cpp

709dd581dd1719727d3235c8cb904775bc300460 authored over 4 years ago by Timo Sachsenberg <[email protected]>
don't print total feature number for every batch

e391ebaee2173e52b36bd57b040c2e765548c0f9 authored over 4 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #18 from OpenMS/timosachsenberg/proteomicslfq-tool-4550

ensure unique id in FFid

23d1dd641c1abe06bb5851f79b2cad216cb1f65b authored over 4 years ago by Timo Sachsenberg <[email protected]>
ensure unique id in FFid

4622376c5b1018e67cc8eabb529ea94e775f0409 authored over 4 years ago by Timo Sachsenberg <[email protected]>
disable warnings for mass tags

de7c2c7b0d5ad37b5c91bde086310d7580c9a4ab authored over 4 years ago by Timo Sachsenberg <[email protected]>
Merge remote-tracking branch 'upstream/develop' into feature/plfq_fixes

0d80c205d7fd1a29319953c05bd7b7eb93daacd8 authored over 4 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #4452 from hroest/feature/aasequence_speed

Feature/aasequence speed

fc56dd1e4cad41ca72c98bf948109c35dc464755 authored over 4 years ago by Timo Sachsenberg <[email protected]>
some minor command line cleanup of plfq and associated tools

f29f0f5eaf60f8c8f555aea12b1ee21fcde62e83 authored over 4 years ago by timosachsenberg <[email protected]>
unordered_map -> map in FLASHDeconvAlgorithm.cpp

98f3750feb48e67a03c9881ed4dbdaebb96676d3 authored over 4 years ago by kyowonjeong <[email protected]>
Update Doxyfile.in

cc27f6a829360b3a3e7bd1b3ec9a1824edf3b6fa authored over 4 years ago by jpfeuffer <[email protected]>
[TEST] fix tests

a480c16780709bab340eabb1f477738164ec65fd authored over 4 years ago by Hannes Roest <[email protected]>
unordered_map -> map in FLASHDeconvAlgorithm.cpp

c9ed71bb2d091f93682f19cd0a2227174b48ed71 authored over 4 years ago by kyowonjeong <[email protected]>
Merge pull request #4556 from OpenMS/fix/FileInfo

corrected FileInfo output of consensus feature

b9924d82205c40867c564e053b476c2802157c62 authored over 4 years ago by Timo Sachsenberg <[email protected]>
- Refactor IDScoreSwitcher to algorithm class and allow requesting

of general score "types"
- Initial version for inference on consensusXML. Does not have all
t...

5851decc79adeb803a78dc605b2e789013f482c3 authored over 4 years ago by Julianus Pfeuffer <[email protected]>
corrected FileInfo output of consensus feature

8f42c3c7e43b6869ddc103f5238822d9b53be5ab authored over 4 years ago by Timo Sachsenberg <[email protected]>
SNR calculation for MS2 triggering implemented. Speed up by optimiation.

6c70d1a264bd8c6fa9c91c3044f49bb5e1556d57 authored over 4 years ago by kyowonjeong <[email protected]>
Update MascotAdapter.cpp

77a7dcc89beb2595380efe860558cd9b876eca03 authored over 4 years ago by jpfeuffer <[email protected]>
Try depending the logic on the in and output types

52d3addd525d2d98537a25e6c7effb84fa1346fb authored over 4 years ago by jpfeuffer <[email protected]>
Merge pull request #4542 from bernt-matthias/topic/novor-mzML-extension

Let NovorAdapter also use mzML

bc191a461f9953fdae4dcfa6f649947a83e99edc authored over 4 years ago by jpfeuffer <[email protected]>
remore wrong mascot_out formats and add input formats

d77dec7e7dcd4394a5f719c246ce3cda06ea76a5 authored over 4 years ago by M Bernt <[email protected]>
fix

664393be8fa535eaacc85c437425522f9889da2f authored over 4 years ago by M Bernt <[email protected]>
MascotAdapter: specify allowed output formats

27db2bd08d4863a25232621cd3de0045903b76a8 authored over 4 years ago by M Bernt <[email protected]>