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

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

ce59617cb0ca05a69c59736db58d8015b60c1276 authored over 4 years ago by Timo Sachsenberg <[email protected]>
Edit badges links

06443c2e361a2c95ec36ccda6244af27402c0399 authored over 4 years ago by jpfeuffer <[email protected]>
Merge pull request #4543 from jpfeuffer/develop

Merge back

d17cc251fd0c4068eb253b03c9fb107897771fdc authored over 4 years ago by Timo Sachsenberg <[email protected]>
Merge branch 'release/2.5.0' into develop

cc284e3031ddf900973cad1866e64bb7af6f47a5 authored over 4 years ago by Julianus Pfeuffer <[email protected]>
Let NovorAdapter also use mzML

78f6f41a029baf7139d1a59846de987bfc91eae3 authored over 4 years ago by M Bernt <[email protected]>
also adapt test to check and remove unused variable

318f9edc82ed9f8a2037f215a6f756ed40340629 authored over 4 years ago by M Bernt <[email protected]>
remove apparently redundant extension

and accept only the one that as commonly used in OpenMS

21968269eeb89a08a54c8101fe14ff3631dc8943 authored over 4 years ago by M Bernt <[email protected]>
real time init

681d535e2ff694c07ee4b34fd92461ba3666d854 authored over 4 years ago by kyowonjeong <[email protected]>
fix doxygen errors (#4534)

* fix doxygen errors

* more fixes

* Update MessagePasserFactory.h

* Update MessagePasse...

f6490426a5b1275d73529bde8721e4dd14cf4468 authored over 4 years ago by Chris Bielow <[email protected]>
TOFCalibration: be more precise in input formats (#4525)

* TOFCalibration: be more precise in input formats

- tof_const is tsv
- ref_masses may also ...

bfb26979a2915643a01be494f6befcd5387b5223 authored over 4 years ago by M Bernt <[email protected]>
small fixes (#4499)

* [LOG] OpenSwath output

* [FIX] bugfix for empty transition set

* old bug -fix

* [FIX]...

bcfe2667f257791074f2196ddb527168fe8e6033 authored over 4 years ago by Hannes Roest <[email protected]>
Check only 1x if output file can be written (#4538)

Happens already here https://github.com/OpenMS/OpenMS/blob/ca57038b730ba5995662476e64b4019130cc0...

a9ca49ad7e944b14015e37232dd05a2dd93326b9 authored over 4 years ago by Timo Sachsenberg <[email protected]>
[NOP] moved changed parameters to file CHANGELOG_PARAMS (#4532)

* [NOP] moved changed parameters to file CHANGELOG_PARAMS

* Added very recent additions to ch...

c270e22308b034a9a5f146146e578a32df62de4a authored over 4 years ago by Timo Sachsenberg <[email protected]>
Store name of float data arrays and unit names (#4537)

* [NOP] cosmetic fixes

* [FIX] fix for crawdad

* [FEATURE] store name of array

* [FIX] ...

ad838ec351e161c7d307963c7fd37d462994152c authored over 4 years ago by Hannes Roest <[email protected]>
Merge pull request #4535 from OpenMS/fix/lfq_seeds

[FIX] quantification based on seeds was broken

e146df5d2d385fa7dcd4c214264c5da659eb9b6a authored over 4 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #4327 from hroest/feature/chrom_by_id

Feature/chrom by

3a83a0e30256f24cc0349ffd25c9a7f1279a8b15 authored over 4 years ago by Timo Sachsenberg <[email protected]>
Update test_MSNumpressCoder.py

4e341405733d5c78caacd306c278d51c6a7db74b authored over 4 years ago by Hannes Roest <[email protected]>
Update FeatureFinderIdentificationAlgorithm.cpp

a4fd3940d81ae7e11ae4ba7d0b67adbef69ec125 authored over 4 years ago by Timo Sachsenberg <[email protected]>
small change in debug part

9eb89a5cd6640ef17a31f1380fb42f15fa13d61f authored over 4 years ago by jpfeuffer <[email protected]>
[FIX] quantification based on seeds was broken

03d4fdddcf3ff31de6dfd6fe67a6559496b8d626 authored over 4 years ago by timosachsenberg <[email protected]>
RTEvaluation: fix output formats

- csv output was not csv so I just made it tsv (which is better anyway)
- latex was missing line...

43f25c4d716180f245be9d467a796246681590a3 authored over 4 years ago by M Bernt <[email protected]>
reactivate debug write of transitions in ffid

03d10d574abf918e49302933b8363acd1dd1c67f authored over 4 years ago by Julianus Pfeuffer <[email protected]>
Merge pull request #4528 from jpfeuffer/feature/ffIDBatches

[Feature] FFID batch extraction of chromatograms

d993cae09f7346647eb849c23b5e65181d9a1e20 authored over 4 years ago by Timo Sachsenberg <[email protected]>
style

48ba841c84b642a5c881ba9bafcb2d1867a1cdca authored over 4 years ago by Julianus Pfeuffer <[email protected]>
param docu

53b45ee3f5b3fb490dca830df25685a7b3623683 authored over 4 years ago by Julianus Pfeuffer <[email protected]>
nop

a8a29451cbc462be736eea646d423be1039a9eda authored over 4 years ago by Julianus Pfeuffer <[email protected]>
docu and names

9ec3315ee9acfb657bf6749afda9d70093021496 authored over 4 years ago by Julianus Pfeuffer <[email protected]>
Added batch size chrom extraction feature to FFID.

9916b75a08cc3f95b08a0ed06900dd6b97a53045 authored over 4 years ago by Julianus Pfeuffer <[email protected]>
update THIRDPARTY

b1f91807af867bd72a346ee2c8c35e1439c361a1 authored over 4 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #4524 from oliveralka/fix/FFM_chrom_error

FFM resolve discrepancy of number of features and chromatograms

640dc60ab790f1169e31d68ef4df4f0e2739255b authored over 4 years ago by jpfeuffer <[email protected]>
chrom fix

3a128f58907bf04de71c90d822e38eff21cc8fed authored over 4 years ago by oliveralka <[email protected]>
Merge pull request #4523 from OpenMS/develop

update release 2.5 branch

5c9357a0cc23fed72e0e3ca75e9d0dc42b85c5c6 authored over 4 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #4508 from sgalkina/before-hdf5

FIA-MS data processing class

ca57038b730ba5995662476e64b4019130cc024e authored over 4 years ago by Timo Sachsenberg <[email protected]>
fixed templates

8bf460cd470ad8153667b7e1d939e8749eca68dd authored over 4 years ago by Julianus Pfeuffer <[email protected]>
fix: default constructor for scheduler

847cc67fc02d8c2329a49266fb3e801e8ea6aea0 authored over 4 years ago by Svetlana <[email protected]>
Merge pull request #4522 from jpfeuffer/fix/precisionTextVsMzTab

[Fix] precision text vs mz tab

25d89575b2c4c4dbe17b91e54f2e2b78bb68558a authored over 4 years ago by Timo Sachsenberg <[email protected]>
fix: remove the namespace

97df5454cf1e7bcd64f5925f6f134fa2889dcb64 authored over 4 years ago by Svetlana <[email protected]>
move the string conversion into the stream operator

fa25849511db298112c07fa5a685158f589ac679 authored over 4 years ago by Julianus Pfeuffer <[email protected]>
Use StringConversion for doubles in TextExporter

d1ece00c453bd70c3aa710d5e380cd5e57729296 authored over 4 years ago by Julianus Pfeuffer <[email protected]>
Merge pull request #4521 from cbielow/doc_mapTree

fix docu for MapAlignerTreeGuided

d1cfcf0264cc1b19aa5d8c87843279ac6b4b2bfd authored over 4 years ago by Timo Sachsenberg <[email protected]>
fix: python bindings objects

2d3be8eb817ebc30bbb754d19dbfa9f6b8a13ee6 authored over 4 years ago by Svetlana <[email protected]>
fix docu for MapAlignerTreeGuided

a9404daaae44a2ec56436024c5cef08b85ac46e7 authored over 4 years ago by Chris Bielow <[email protected]>
fix: python bindings, double to float convertions

c82dbed55886872ddd1f9d95e05ff4ab5764d641 authored over 4 years ago by Svetlana <[email protected]>
update TRFP in THIRDPARTY

204a3e9e5b290e1fd42cb58c9f502450f0223251 authored over 4 years ago by Timo Sachsenberg <[email protected]>
Merge branch 'release/2.5.0' of https://github.com/OpenMS/OpenMS into release/2.5.0

a52cae64afa3f639714eace0c21f9ac55984f9fc authored over 4 years ago by Timo Sachsenberg <[email protected]>
fix: integer type for OpenMP

1f3e20262461bb279eacc928cf56b6c1ca005aed authored over 4 years ago by Svetlana <[email protected]>
Update .gitpod.yml

df1e0ba5712eaadb8d25c3e4bca3db091fc5e428 authored over 4 years ago by jpfeuffer <[email protected]>
fix: failing builds

09dcf0ebf42d8f2986fdc7cba3576b0607e71a53 authored over 4 years ago by Svetlana <[email protected]>
Merge pull request #4506 from jthueringer/MapAlignerTreeGuided

[FEATURE] new map aligner: MapAlignerTreeGuided

e5ae8847ccd8e215555b78fac5c6789af07a0e2c authored over 4 years ago by Chris Bielow <[email protected]>
fix: test

0340ec02643a85f387d64d8736e01e8fcd0020ed authored over 4 years ago by Svetlana <[email protected]>
Merge pull request #4517 from cbielow/doc_FFcentroided

Doc FFCentroided

4222921ee7bf358de1bcff2b860d08980c045944 authored over 4 years ago by Timo Sachsenberg <[email protected]>
fix: test builds (peak picking, style)

f1149d139c2c726b12e57446e6ec3a3058100b93 authored over 4 years ago by Svetlana <[email protected]>
doc: specify the classes used internally; performance optimizations

955eeda59733bd969d29cddf553acb823bd4a012 authored over 4 years ago by Svetlana <[email protected]>
Merge branch 'develop' of https://github.com/OpenMS/OpenMS into doc_FFcentroided

# Conflicts:
# src/openms/source/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderAlgorithmPicked.cpp

9ff481569081805057c9316fc33d5c5922248cc0 authored over 4 years ago by Chris Bielow <[email protected]>
better info message for FFcentroided. Fixes #3974

d245c893bbc514703fcf11c20ee1c4dc14e24b65 authored over 4 years ago by Chris Bielow <[email protected]>
fix: pyopenms imports

cb2660f609f66a210be8e210b31e3a6df38288f0 authored over 4 years ago by Svetlana <[email protected]>
Update ProteomicsLFQ.cpp

525262abfd18c70425cf9bb4966d111779274a9e authored over 4 years ago by jpfeuffer <[email protected]>
test: merge and pick steps from fixtures for a chunk of the serum test file

30091b33b6e711f7713a782791bef17d736567dc authored over 4 years ago by Svetlana <[email protected]>
Merge pull request #4516 from jpfeuffer/fix/idpep_outliers

[Fix] idpep outlier handling

e0c44298b73784e696d1101832b1ad523c61519a authored over 4 years ago by Timo Sachsenberg <[email protected]>
add extreme percentile removal as option

35eda7d50040f599c23a0c60488af9866c1cf024 authored over 4 years ago by Julianus Pfeuffer <[email protected]>
py tests

384b006f1710d4441edbe83c9fe470740a5828b7 authored over 4 years ago by Julianus Pfeuffer <[email protected]>
py bindings again

e5ebcc71074a8cb10b22dbfe29020277e15e328f authored over 4 years ago by Julianus Pfeuffer <[email protected]>
py bindings.

e0cfa8a5cad6b18891bc7d575027c2422c07e0e4 authored over 4 years ago by Julianus Pfeuffer <[email protected]>
Forgot to adapt test sources.

ccab340c5f13b16cbf976732046f294c8c137f3f authored over 4 years ago by Julianus Pfeuffer <[email protected]>
Introduce outlier removal in IDPEP

93717311220975025ab4e9df1f4898be6d72bb95 authored over 4 years ago by Julianus Pfeuffer <[email protected]>
as suggested by Chris Bielow

* changed paths of include
* changes in the documentation
* added formula for the calculation of...

0427cb0cf790bf1fab486131396d784620aa8f15 authored over 4 years ago by JuliaThüringer <[email protected]>
minor speed up

01b2619c08a6984512fbeabcfaec250a1cb1e031 authored over 4 years ago by kyowonjeong <[email protected]>
add valid file formats for input file reannotation

0833249f161a75a970ae636e0181537faaaf1f1b authored over 4 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #4515 from jpfeuffer/fix/proteomicsLFQ_FDR

[Fix] proteomics lfq fdr

dfa3506be1fea4d237793fbe5293ff0228fae542 authored over 4 years ago by jpfeuffer <[email protected]>
Better FDR control and correct filtering orders

f5b3d234465146792926d399115fb0bbcf3d1bd1 authored over 4 years ago by Julianus Pfeuffer <[email protected]>
update THIRDPARTY to include TRFP 1.2.0

90167f584320bbc45a77b0b617854810578b9b98 authored over 4 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #4513 from oliveralka/add/AGM_framgent_restriction_to_250

AssayGeneratorMetabo: Filter fragments based on min/max m/z (release 2.5.0)

20dc6c56a2b43d28f45980e10f64441e9216f75f authored over 4 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #4507 from cbielow/code_of_conduct

an initial version of a Code of Conduct

251405703a4f200fb924c4c8f0cd2696316d6944 authored over 4 years ago by Timo Sachsenberg <[email protected]>
feat: load picked spectrum from cache

29c8c5119287a35f8782d42d333f1e2cec124857 authored over 4 years ago by Svetlana <[email protected]>
output file / message polished

22b9b34c2972030c359d8403ed9bc846ac134bb4 authored over 4 years ago by kyowonjeong <[email protected]>
MS2 frag isotope estiamtion removed. Input parameters polished. The bug in overlapping resolved..

8afa24d9e7d65a3d87583e81d207e6cd8d7abd8b authored over 4 years ago by kyowonjeong <[email protected]>
[FIX] tests, pxd, [ADD] restriction test

cc30ee341dd43410e14aded42646f4085ca78305 authored over 4 years ago by oliveralka <[email protected]>
[FIX] Inital param - do not place restrictions on fragment masses

0cf25f64812d72dccc5271d1f3d3bb0ef03e06ff authored over 4 years ago by oliveralka <[email protected]>
[ADD] Filter fragments based on min/max m/z

6921d3f1a98f7775bff32c5c53873c71832a5fb5 authored over 4 years ago by oliveralka <[email protected]>
update thirdparty to include signed sirius libs

65321984877face86f606d6cdb876fb497ab9f8a authored over 4 years ago by Julianus Pfeuffer <[email protected]>
Update TP to HEAD

c366f0066c6a0977923e5f9175852f3b346a7ac9 authored over 4 years ago by Julianus Pfeuffer <[email protected]>
Note on notarization issues on macOS

7d9b030bd2d0dc5c7fc229a2176add13ad6fb8d9 authored over 4 years ago by jpfeuffer <[email protected]>
feat: python bindings

624802773d98820772efec6694c5a755655cc8ca authored over 4 years ago by Svetlana <[email protected]>
Merge pull request #4511 from enetz/fix/IDView_ppm_error

[GUI,FIX] precalculated ppm errors were always read from the first PeptideHit

97aa06cf48cf49f93ac5413a34e879b22bec0e9c authored over 4 years ago by Timo Sachsenberg <[email protected]>
Merge branch 'before-hdf5' of github.com:sgalkina/OpenMS into before-hdf5

661c0b5fe167b77e8f6b6c87172aec6a1c4fe973 authored over 4 years ago by Svetlana <[email protected]>
chore: clean unused includes

2a8f819f5ac46349c1c579fc505cb3b2d4b17783 authored over 4 years ago by Svetlana <[email protected]>
Merge branch 'develop' into before-hdf5

eb7a3c065c2e8d083583d2dc2677209827feffcf authored over 4 years ago by Svetlana Kutuzova (Galkina) <[email protected]>
fix: resolve the conflicts

c6356628b303c937068ac7867064d2845423a6a9 authored over 4 years ago by Svetlana <[email protected]>
doc: dyoxygen documentation

6bdd8633990b0f6fdcbae47015729761eca9d87d authored over 4 years ago by Svetlana <[email protected]>
MS2 frag isotope estiamtion applied only when necessary

56d5677e471042fb5022f84e2b0634e9c3855b34 authored over 4 years ago by kyowonjeong <[email protected]>
[GUI,FIX] ppm errors were always calculated from the first PeptideHit

f465bdea1175a17ee28322275d71d56c4f47905a authored over 4 years ago by enetz <[email protected]>
chore: scheduler in the separate file

e7d285f468acb0e45f612d939a90c0dda75b9d76 authored over 4 years ago by Svetlana <[email protected]>
feat: default parameters handler

0767dc6b82a476c4ee34add261f4ba7390456bf8 authored over 4 years ago by Svetlana <[email protected]>
MS2 frag isotope estiamtion applied. Should be improved..

eb62b6b90ad80b0cfd14119eba52f12767d8cd86 authored over 4 years ago by kyowonjeong <[email protected]>
Gitpod task error?

3e3532baf57da90d83a2695fb845d9d668a1ed2a authored over 4 years ago by jpfeuffer <[email protected]>
further link to CoC

10919983080b8c4c7ad31e97c229edcf65852b6b authored over 4 years ago by Chris Bielow <[email protected]>
test gitpod prebuild

076abdb22efab359f4aeb0af99dd5c9ac85ab29d authored over 4 years ago by jpfeuffer <[email protected]>
Update .gitpod.yml

318cdf8da55bffd2d567ec7fc3abd2db32e4fee4 authored over 4 years ago by jpfeuffer <[email protected]>
Update .gitpod.yml

ea88e836b1b950f74737613f5f2c12e6e509252a authored over 4 years ago by jpfeuffer <[email protected]>
Update README.md

6cd707ad22ef98b04d0e948dd3f3f7a2b90a882f authored over 4 years ago by jpfeuffer <[email protected]>