Ecosyste.ms: OpenCollective

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

github.com/OpenMS/OpenMS-1

The codebase of the OpenMS project
https://github.com/OpenMS/OpenMS-1

[FEATURE] Add iBAQ to ProteinQuantifier (#6107)

* update

* added iBAQ to ProteinQuantifier

* removed outdated iBAQQuantitation.cpp

* re...

ab260e1aad2b23c81ea50a62f3ebf69b6b7a6a13 authored over 2 years ago by Matteo Pilz <[email protected]>
infra-fix: don't lint deleted files (#6172)

3af93c27d4b96291498e41cb24aaf3b9b81cbe0b authored over 2 years ago by Simon Gene Gottlieb <[email protected]>
Merge pull request #6171 from SGSSGene/fix/github-workflow

Fix/GitHub workflow

9cea4b51096f54e6823545d185a047676f89eb51 authored over 2 years ago by Julianus Pfeuffer <[email protected]>
update: github workflow uses tj-actions and DoozyX

005a0fbb958dc7926f96f53561d28245bb4b4dda authored over 2 years ago by Simon Gene Gottlieb <[email protected]>
infra-fix: don't lint deleted files

ea6a0f18f06b851c5b85a85782ac4425abba57ee authored over 2 years ago by Simon Gene Gottlieb <[email protected]>
fixed indentation and replaced {cpp} and {sh} with {.cpp} and {.sh} as discussed

4c030a2659c9ac2176c93e38d91bc903b892ea6c authored over 2 years ago by greengypsy <[email protected]>
add peptide level fdr/q-values (#6132)

* add peptide level fdr/q-values

* use emplace

* add option to enable/disable FDR calcuati...

5f93c53c7201a8a84d5475354a8b27a50a006655 authored over 2 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #6169 from axelwalter/fix/GNPS-meta-values-from-consensusmap

[Fix] GNPSMetaValueFile get mzML file names from ConsensusMap

8e4aae3815c7a0dcd8ba6a03143af5b07f56cbe0 authored over 2 years ago by axelwalter <[email protected]>
Merge branch 'develop' into feature/searchSpectrum_extended

25837556a8b3ef717a93d88a81eb198a5b2c18f2 authored over 2 years ago by Timo Sachsenberg <[email protected]>
alternative method to get mzML file paths

1181dd2e6c422fb34033d7441d1c9133f013d796 authored over 2 years ago by axelwalter <[email protected]>
update tests

1154c77a2ef8d1e332bfd1897116fb4d576fd0ed authored over 2 years ago by axelwalter <[email protected]>
use ConsensusMap as input for GNPSMetaValueFile

654dee6b85e9b8664112c5bcfecd412afafb1e5b authored over 2 years ago by axelwalter <[email protected]>
Merge remote-tracking branch 'upstream/nightly' into feature/FLASHDeconv

38c66f5403e103663469d17ccfcf92e89d3cbd6e authored over 2 years ago by JeeH-K <[email protected]>
Merge remote-tracking branch 'upstream/develop' into delete-dups

03fb606803db8a29ef0aa9fa32535dbc263b583f authored over 2 years ago by Tapasweni Pathak <[email protected]>
update changelog

fb509babb544916254ba534329286c1d430dceaf authored over 2 years ago by Tapasweni Pathak <[email protected]>
Delete: duplicate pages in openms rtd and doxgen

Ref: https://github.com/OpenMS/OpenMS-docs/issues/4#issuecomment-1125150286.

22141b3490deb89eb85948a960c527b8d93d1ccc authored over 2 years ago by Tapasweni Pathak <[email protected]>
made changed to documentation according to feedback

a36baf23b48e8bb81e06f9d7e90f6b6a92c299b6 authored over 2 years ago by greengypsy <[email protected]>
Merged develop and added metavalue num_of_datapoints.

f9f4581bd9c9e64fcd2842288a6354a313996041 authored over 2 years ago by Virginia Rossow <[email protected]>
Merge branch 'develop' into maxquant-output

72209fc950fef1c32a22502d03193d69ab5d5292 authored over 2 years ago by Virginia Rossow <[email protected]>
Added the compatible version of MSFragger into the MSFraggerAdapter documentation. (#6154)

a686a995efc5d2f38519666039d856566a571654 authored over 2 years ago by tillenglert <[email protected]>
Feature/GNPSexport_split_files (#6152)

* Separate class for GNPSQuantificationFile and adding GNPSMetaValueFile

* add new files

*...

1acb92a7d2ded2f5fc706045be36b6bf87ca1f5b authored over 2 years ago by Timo Sachsenberg <[email protected]>
fixed signed and unsigned int comparison (#6150)

Co-authored-by: Timo Sachsenberg <[email protected]>

988bfef13dd389a6b973bc70e0b4c35b70d6c320 authored over 2 years ago by KyowonJeong <[email protected]>
[PARAM, FEATURE] FileConverter, disable zlib compression flag (#6151)

db0229516839ba59004032f0b9e04ab553bb81a6 authored over 2 years ago by Eugen Netz <[email protected]>
fix unneded pragma warning in cpp (#6148)

ac113412ef7524d51f648e696f81fecceab3de98 authored over 2 years ago by Timo Sachsenberg <[email protected]>
added pull request checklist link

de5d92d770adcd488b2ccb8392d09bc1f61cf064 authored over 2 years ago by greengypsy <[email protected]>
modified developer-faq to include questions not included in contributor-faq.md

40c0a14276cf1b574960dae58c60f37701fbe76a authored over 2 years ago by greengypsy <[email protected]>
Merge pull request #6136 from zhuchcn/uclacds-develop

Add support of "no cleavage" for XTandemAdapter & CometAdapter

1f903c020948ae0ddfea70b21440047b6e328c23 authored over 2 years ago by Julianus Pfeuffer <[email protected]>
fixes

8952f5f98e7f710aa19a008d79495a9e2766dce4 authored over 2 years ago by bielow <[email protected]>
Merge branch 'develop' of https://github.com/OpenMS/OpenMS into refact_toppview

# Conflicts:
# src/openms/source/CONCEPT/CommonEnums.cpp
# src/openms_gui/source/VISUAL/ANNOTATI...

0f637941b4db69b8f22e4c0dbf9d107c63c8f538 authored over 2 years ago by bielow <[email protected]>
progress...

66c4132380f901ad57954d8932770939ee426f5e authored over 2 years ago by bielow <[email protected]>
added discussed doxygen files

572a9a2a218b67a407e401707474562947cb6e56 authored over 2 years ago by greengypsy <[email protected]>
Msms works + test added

abdc0a9d2658a5d4eac7d3393397b3d3737aceb3 authored over 2 years ago by Virginia Rossow <[email protected]>
Merge branch 'OpenMS:develop' into develop

969cf912d2adb7a8c0bc3430ddc85a85a0cb0a35 authored over 2 years ago by greengypsy <[email protected]>
Merge pull request #6141 from cbielow/api_extensions

some preps for upcoming GUI PR

e0e8d0ebdd89b5f43cda84b5a6548d5af6772a9e authored over 2 years ago by Chris Bielow <[email protected]>
MQEvidence Test now working with fasta

9c865feb468d5ed941f854a971fca676421ea2ee authored over 2 years ago by lennykovac <[email protected]>
add tests

6e9dda69331a78b2555281bb2774899c4dad02d9 authored over 2 years ago by bielow <[email protected]>
some preps for upcoming GUI PR

f00d103293359325e18ff849043a5c15af592753 authored over 2 years ago by bielow <[email protected]>
some small changes

fa4a6e170f2a0eb477a88773d7a92f3ce6c788dd authored over 2 years ago by beschorneh32 <[email protected]>
Merge branch 'maxquant-output' of https://github.com/vrossow/OpenMS into maxquant-output

a9b0a23255ea15e0f9e00978432a9c039ab48394 authored over 2 years ago by beschorneh32 <[email protected]>
MQEvidence completely uses MQExporterHelper

2918d8a06ac709f73b15e32fb59e4dede7e55020 authored over 2 years ago by beschorneh32 <[email protected]>
Fix (EnzymaticDigestion): exact match for SPEC_FULL and no_cleavage onlyh when allow_random_asp_pro_cleavage is false

4e929a2092b0ecaed1da149648ea49294a72686f authored over 2 years ago by zhuchcn <[email protected]>
added option to remove hulls

8f6165f5f2f203acada107b32c5721a243d5202a authored over 2 years ago by Timo Sachsenberg <[email protected]>
lots of fixes

b6bec7806be31c07346a40b69636cb3a4164d87d authored over 2 years ago by bielow <[email protected]>
lots of fixes...

d586cbf770b8a7d2d8f06cdf9e202aa8b86536e1 authored over 2 years ago by bielow <[email protected]>
Test function + a few documentation needed

f9eb425b7125515e2a0ae5513513f67f63d507fa authored over 2 years ago by kyowonjeong <[email protected]>
Msms should work now.

287f947cb574349ec93703e31cd48e5fd2dee674 authored over 2 years ago by Virginia Rossow <[email protected]>
Merge branch 'maxquant-output' of https://github.com/vrossow/OpenMS into maxquant-output

dd6d4b6a8e1f5462ed40f9b92e4271df4c17fffc authored over 2 years ago by Virginia Rossow <[email protected]>
fixed the TOPP_QualityContorl_1 test, by adding the new input fasta_file

c03dade94f7a5d725b8faa5dfba2128754cd6827 authored over 2 years ago by lennykovac <[email protected]>
Test function + a few documentation needed

92b7295e739519dd32ade9b1dad2289c54f85e4d authored over 2 years ago by kyowonjeong <[email protected]>
Merge branch 'maxquant-output' of https://github.com/vrossow/OpenMS into maxquant-output

836a67a821000a6dd5117cae30591182acb5e871 authored over 2 years ago by Virginia Rossow <[email protected]>
change log updated for "no cleavage" of CometAdapter & XTandemAdapter

91691164ba3fb41d5bbb8702ec4528da7244282d authored over 2 years ago by zhuchcn <[email protected]>
[FIX] DatabaseSuitability Tests only executed when CometAdapter is found (#6134)

* additional CMake variable for finding CometAdapter

* forget 'endif()'

* reverting accide...

586fdefb965f2108d8f96803eb1e57fea7d46786 authored over 2 years ago by TomW <[email protected]>
Metavalue number of datapoints (#6128)

* initial change to get the new metavalue number_of_datapoints

* found a very stupid mistake ...

d4a5b32e04c565bc1c0d012994cea12697e2e1be authored over 2 years ago by Virginia Rossow <[email protected]>
getting 1d layers to work

0381e04bd15252f3d90a5291c2105bed4e8964e7 authored over 2 years ago by bielow <[email protected]>
Addressed Chris's comment : move file write parts to FORMAT.

9d8971f4edf6738f1f891cdd82d1d1aaa86c56a9 authored over 2 years ago by kyowonjeong <[email protected]>
Addressed Chris's comment : move file write parts to FORMAT.

39acc2e27cb3fb41f0001100308e6e7f3d7e3845 authored over 2 years ago by kyowonjeong <[email protected]>
fixed some errors with MQExporterHelper

b84a6b93003cf729acc3d539123565b5ac77ab01 authored over 2 years ago by beschorneh32 <[email protected]>
Merge pull request #6091 from jpfeuffer/feat/specAnnotationSirius

[FEATURE] Export annotated spectra from Sirius as mzml

9b5a8e0de00c1a257d84c0cd9a01a42b6ef1fa2b authored over 2 years ago by Julianus Pfeuffer <[email protected]>
Merge branch 'develop' into feat/specAnnotationSirius

b4ba11b797e3773449b6e799a22720c0e091ca11 authored over 2 years ago by Julianus Pfeuffer <[email protected]>
fix: added precursor mz comparison for annotateSpectra

3b9eb35e6b90ab34431d39a84fd65a5ef4aba85b authored over 2 years ago by dmccloskey <[email protected]>
Merge remote-tracking branch 'upstream/develop' into uclacds-develop

3f8466d0f6a2b0690e46b4af793abbe5f1059340 authored over 2 years ago by zhuchcn <[email protected]>
pyopenms

e8aad846b74b6b998288725329b640c82937ca72 authored over 2 years ago by Julianus Pfeuffer <[email protected]>
add 1DChromLayer

57192a0fe83df487e34edd94c2a2a7507ba542ff authored over 2 years ago by bielow <[email protected]>
Addressed Chris's comment : move file write parts to FORMAT.

3cb7cf591e9f09c1050389a17774aa880e8cc2c1 authored over 2 years ago by kyowonjeong <[email protected]>
Merge branch 'maxquant-output' of https://github.com/vrossow/OpenMS into maxquant-output

69e554fbb8ec105eea8b3d4e42e5bd83100fc3a4 authored over 2 years ago by Virginia Rossow <[email protected]>
Disable indeterministic tests on other platforms.

14c6c6be0537ad82407865a1573164377497e26b authored over 2 years ago by Julianus Pfeuffer <[email protected]>
some work on helpers and started using the helper in MQEvidenceExporter

ab94d434e8aacd5ce05bc20ead586591d28be3f7 authored over 2 years ago by beschorneh32 <[email protected]>
changed msms further

85e57b86664a90320114a90da540170052b860c4 authored over 2 years ago by Virginia Rossow <[email protected]>
Add tests and refactor user param names

181e36f14fe9ec11aff9531b71bd4aacc414361f authored over 2 years ago by Julianus Pfeuffer <[email protected]>
rename

fc8b7c061ab5f06e02981cfba962500187eb6242 authored over 2 years ago by bielow <[email protected]>
move code for projections into Layer

12735be2cd10ce7a80aa6f5d21d02f67d9923bf3 authored over 2 years ago by bielow <[email protected]>
working evidence & quality controll, need to addapt the tests

47e7137df5d7190eed3501a00d1e11c7369682c1 authored over 2 years ago by lennykovac <[email protected]>
Merge remote-tracking branch 'origin/feature/FLASHDeconv' into feature/FLASHDeconv

# Conflicts:
# src/openms/include/OpenMS/FORMAT/sources.cmake

acc2f1f8ad064c6dafbc20080f8303d2b350328a authored over 2 years ago by kyowonjeong <[email protected]>
SpectraMerger: recover lost codes from FLASHDeconv branch during merge

201e842f86443780c26e14f907611bdc405a3bda authored over 2 years ago by JeeH-K <[email protected]>
Move FLASHDeconv file outputs under FORMAT

7a709caed8c79c4bd4fa5d050192aecf2d2f819d authored over 2 years ago by kyowonjeong <[email protected]>
Merge remote-tracking branch 'upstream/develop' into feature/FLASHDeconv

03e9b7ae12e22179521d772cfdc7fff06d055065 authored over 2 years ago by JeeH-K <[email protected]>
Merge pull request #6122 from bernt-matthias/sirius-workdir

SiriusAdapter: do not change in the executable dir

89dd3df90df49d5374c4920b28210de125e2154c authored over 2 years ago by Julianus Pfeuffer <[email protected]>
reverse changes to findHit and some changes to MQExporterHelper

44dcff30d8a801abb88eaf102d94d44e43d69b3f authored over 2 years ago by beschorneh32 <[email protected]>
Merge branch 'develop' into feature/searchSpectrum_extended

69c9d5a2460acf64b043d5a3a4e01d695523cfe2 authored over 2 years ago by bertrandboudaud <[email protected]>
FLASHIda beta+, Sean's comments

00d888c64306f5e83140133bca3acf7c6f9e1c45 authored over 2 years ago by kyowonjeong <[email protected]>
Merge pull request #6127 from axelwalter/feature/FFMID-num-masstraces

[Feature] Add num_of_masstraces meta value to FFMID

23a774211f662341e15882c0c85722e8e330d5e0 authored over 2 years ago by axelwalter <[email protected]>
add num_of_masstraces to constants

beff1c8f768ca28e906e05b6858550a56fddee42 authored over 2 years ago by axelwalter <[email protected]>
first implementation of helper class for MQ Exporter

a496352f20042607bdbde91b5fe725e964009c46 authored over 2 years ago by beschorneh32 <[email protected]>
update test output file

37638923d1ce5aac3de61db31ad4c8a90cf7f925 authored over 2 years ago by axelwalter <[email protected]>
correct mv name

907e43138a8b373cc55cb113190a416d87735062 authored over 2 years ago by axelwalter <[email protected]>
add num_mass_traces to FFMID

fb7c0272731f099516ed0ee0e13874137cfd5c64 authored over 2 years ago by axelwalter <[email protected]>
cleanup includes

merge void Plot1DCanvas::saveCurrentLayer(bool visible)

0aec74c469dad5c11e76040507ee68f911dcceeb authored over 2 years ago by bielow <[email protected]>
Merge pull request #6125 from OpenMS/jpfeuffer-patch-1

[FIX/PYOPENMS] update min. req. autowrap version

0a2f20cb6f3c92ff19a1cb758e3c5957e2e3a363 authored over 2 years ago by Julianus Pfeuffer <[email protected]>
Merge branch 'develop' into feat/specAnnotationSirius

0d16b7b855af8a562bfbedc22784f2c8775155b6 authored over 2 years ago by Julianus Pfeuffer <[email protected]>
Add tests

a2527a51b47ac4c2d1e6a2e22fc74413e923f73c authored over 2 years ago by Julianus Pfeuffer <[email protected]>
[FIX/PYOPENMS] update min. req. autowrap version

fixes #6124

7c1f1f32e5f8a13fca2491de749acc99e6deee0c authored over 2 years ago by Julianus Pfeuffer <[email protected]>
[Feature] dynamic tool load (#5877)

* add executable function

* add possibility to search for executables in folder

* Rebase o...

764cb04ff5bf9cfab9e1346b0db004b6f25c11ed authored over 2 years ago by Ruben Grünberg <[email protected]>
Merge pull request #6123 from bertrandboudaud/fix/log_thread_issue

Fix/log thread issue

a66d710d5ba77c329d1fb9d5bc0100b324a51bab authored over 2 years ago by Julianus Pfeuffer <[email protected]>
a visitor for saving layer data

396aae31f2134afd78e2711710b8b03288d3a075 authored over 2 years ago by bielow <[email protected]>
Merge branch 'maxquant-output' of https://github.com/vrossow/OpenMS into maxquant-output

aee16ddec3844b564660f55b5c4f8b0477d1f636 authored over 2 years ago by lennykovac <[email protected]>
redesigned the annotation, TODO the MQeveidencetest and some minor refining

0f19f4cb04d28e4785a00cedc75c3d36c4914b1e authored over 2 years ago by lennykovac <[email protected]>
Merge branch 'develop' into sirius-workdir

190dd7504a4434fd7823e3cb32c1ffb893fc0462 authored over 2 years ago by Julianus Pfeuffer <[email protected]>
Update PULL_REQUEST_TEMPLATE.md

d66eaa6e4bd87ad8f174a8bb8386e26ce77dd422 authored over 2 years ago by Julianus Pfeuffer <[email protected]>
Added change log entry to describe fix

e9169b89cf7824b71517dd64413bc466851faaa6 authored over 2 years ago by bertrandboudaud <[email protected]>
Using same name for omp critical sections

7aa133547a97c1bd274667f44d9884a7cbc183db authored over 2 years ago by bertrandboudaud <[email protected]>