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

[TEST] fix TOPP test

243a4d7194b64982726c0c13dd73346ea78d3129 authored over 5 years ago by Lars Nilse <[email protected]>
[FIX] Silently install Redists (#4046)

Seems like Microsoft loves to change their parameters for silent installs:
http://asawicki.info...

a8597c8d7d90abd4e55eec9042519f72b5ca10f8 authored over 5 years ago by jpfeuffer <[email protected]>
[INTERNAL] write mz and rt from feature handels in cXML to mzTab

443ead7d7ef43a3ded8aa4e31eb2d8bd45e671eb authored over 5 years ago by Lars Nilse <[email protected]>
Update MetaboTargetedAssay.pxd

943c219b77ad830b950483463eeedad4e3c73120 authored over 5 years ago by Hannes Roest <[email protected]>
sum log intensity as score

85869fad0a902abc5578739b0e6c752ba5308dbd authored over 5 years ago by kyowonjeong <[email protected]>
TopNoverRT all

cc0b64b6c06c929e416c350b879cb9e7842fa812 authored over 5 years ago by jschmacht <[email protected]>
RTAlignment first correction

c7a8f870510907bf6070a2ebe485a5a5eefe395a authored over 5 years ago by jschmacht <[email protected]>
insert DataProcessing to MSExperiment for checking Calibration, check Calibration in MZCalibration, modified tests

f7eac98ba2ea32e4c056572b6aa2752937d899f9 authored over 5 years ago by jschmacht <[email protected]>
Merge pull request #4045 from DennisGoldfarb/fix/FeatureFinderMultiplex_singleSpectrum

Looks good. Thanks for the tests.

1f7036bda8c48bec7217a4c455f62073cb85b8bb authored over 5 years ago by Lars Nilse <[email protected]>
[TEST] updated test files, because the order of MetaValues changed

7a3091ca5807acf6cd8fcd741c56fba0744b5f5e authored over 5 years ago by enetz <[email protected]>
[FIX] simplified ID post-processing

9d509f91a9a88065f68b5437d2ccbe36ab040f42 authored over 5 years ago by enetz <[email protected]>
sum log intensity as score

4aed744effaca0b711921d10973e2498835cd9c7 authored over 5 years ago by kyowonjeong <[email protected]>
Test incomplete, more peaks matching problem solved

493f3d6d3b5dd5525d5acbc9a1e49eb148776305 authored over 5 years ago by swew98 <[email protected]>
[REFACTOR] FeatureMapping

b91871bc98f1de9f66319a1d23f6dc724883e3aa authored over 5 years ago by oliveralka <[email protected]>
Duplicated pg removed due to consecutive mass bins

2058b2babf59b6494ee031f56e895d37ffd6623d authored over 5 years ago by kyowonjeong <[email protected]>
Duplicated pg removed due to consecutive mass bins

54e99f402b6548e9592469392c8e5f15d77365ee authored over 5 years ago by kyowonjeong <[email protected]>
[FIX, TEST] fixed the fix for peak area calculation on a single spectrum. Updated regression tests.

63427bcf612cbedadfa4269ec5446992453f603c authored over 5 years ago by DennisGoldfarb <[email protected]>
reset contrib

cfa7f53c3517d4ae6fd2f5f8f8dfcc1c9107e1a6 authored over 5 years ago by DennisGoldfarb <[email protected]>
[TEST] Added a single spectrum regression test for FeatureFinderMulitplex. Updated a previous regression test for the same class. Two additional features were identified.

fa3920e2465033f776a8479af8ecaa70ec6b62e5 authored over 5 years ago by DennisGoldfarb <[email protected]>
[TEST] python bindings

04e44ea4a62b6535c3571770cbc295144d904f55 authored over 5 years ago by oliveralka <[email protected]>
[FIX] Fixed area under the curve for single specturm chromatogram in featureFinderMultiplex

f909b60bd2c8f2fea0a66ef20d8eb7510f5c9faf authored over 5 years ago by DennisGoldfarb <[email protected]>
Duplicated pg removed due to consecutive mass bins

83ccbf75754a6582142aa0f5794aa8eeed42079d authored over 5 years ago by kyowonjeong <[email protected]>
Duplicated pg removed due to consecutive mass bins

e565e829ef72191fa036ebc56151f86d4e1690d4 authored over 5 years ago by kyowonjeong <[email protected]>
Duplicated pg removed due to consecutive mass bins

69e88b841dc1bc8c512c314efb17f04ceab96a83 authored over 5 years ago by kyowonjeong <[email protected]>
float log2 intensity works great

79504a7a26cdc066f6dce176aa2e5c2ccde8e2d0 authored over 5 years ago by kyowonjeong <[email protected]>
[PYOPENMS] added bindings for new OPXLHelper functions

c082a7fb77db7e14310b74dad601dc34dc38d254 authored over 5 years ago by enetz <[email protected]>
[FIX] OPXL: add only needed additional meta values to parsed xquest.xml files

cfb73a29d77ff4e2235e184800c1b147c3ca1b60 authored over 5 years ago by enetz <[email protected]>
[TEST] adapted XFDR test files to removal of broken protein position info

08adce79b6358d45ac701a1607820743b3b27d6a authored over 5 years ago by enetz <[email protected]>
[FIX] OPXL: extratcted some OPXLHelper functionality into separate functions

Made the post-processing of PeptideHits more modular, because some parts of it do not apply to p...

673d10bf9551da1f9add30ec84ccd73e136d5434 authored over 5 years ago by enetz <[email protected]>
added metrics to topptool

203a832ae710f7cc8493139e3e37d862fe394fa9 authored over 5 years ago by Dominik Sebastian Schmitz <[email protected]>
shorter test, dataProcessing exception do not work

bb0f624a00205e48fc4445a91fa9a5a4dc0f425b authored over 5 years ago by jschmacht <[email protected]>
Merge branch 'develop' of https://github.com/cbielow/OpenMS into develop

07a11b30c355fcc7e5592d4125df377526bbffc0 authored over 5 years ago by TomW <[email protected]>
float log2 intensity works great

d83f2c1563088edc5d13332e3b7605238f8daff7 authored over 5 years ago by kyowonjeong <[email protected]>
TopNoverRT first version

246dbd20c97bad07f1271ea7cb6b1f1acc325f7f authored over 5 years ago by jschmacht <[email protected]>
float log2 intensity works great

9eb359e3fe8fc863cd0b162f2f77a326ef88391e authored over 5 years ago by kyowonjeong <[email protected]>
....

2d1e8d84f902b380bd0da4012139d91c7426f869 authored over 5 years ago by kyowonjeong <[email protected]>
lockfree generation of modified peptides (#4036)

* [FEATURE] lock-free modified peptide generation

* Update src/openms/source/ANALYSIS/RNPXL/M...

fd4eac86b817099b90290135a6037de965ed0589 authored over 5 years ago by Timo Sachsenberg <[email protected]>
merge upstream

552f78e9740e10e013920f43ac1f212689307725 authored over 5 years ago by Chris Bielow <[email protected]>
Merge pull request #49 from OpenMS/develop

Merge upstream

6c8a3eacff1e02435d21d91fb695c29115783c52 authored over 5 years ago by Samuel Wein <[email protected]>
[FIX] add missing method description

6c3701ec41cbb3508a43b53d124b2ff9176fb761 authored over 5 years ago by oliveralka <[email protected]>
[FIX] asked changes, addes charge to precursor, fixed issues with

SiriusAdapter

4c4f2dcf294177ef9a7e4c8fe74b4abad57b480c authored over 5 years ago by oliveralka <[email protected]>
works great for yeast

8e593f34e3b02e85ed84c1a496146371ddd6e0cb authored over 5 years ago by kyowonjeong <[email protected]>
Feature/test move (#4043)

* [TEST] add tests for move operators

* [FIX] fix operator<<, add test

* [FEATURE] DateTim...

2d6653819e972d3573c102b243f646d3412262c4 authored over 5 years ago by Hannes Roest <[email protected]>
works great for yeast

09e55218d2b82f226bd2edbe86c722df2c7ec632 authored over 5 years ago by kyowonjeong <[email protected]>
works great for yeast

ddfb0d0c2c416e591544858572232db00b2bd09c authored over 5 years ago by kyowonjeong <[email protected]>
works great for yeast

94fd022761cbb1b8dbd957a3abdb09222c9cbef2 authored over 5 years ago by kyowonjeong <[email protected]>
works great for yeast

76889ca9af483d33cf3d4840bb5cc0d7a296fbff authored over 5 years ago by kyowonjeong <[email protected]>
[ADD] MSstatsTMT support in MSstatsConverter (#4039)

* [ADD] draft MSstatsTMT in MSstatsConverter

* [ADD] Unmodified sequence for MSstatsTMT, add ...

bfdab3eee232b6b212551bbc3b5f723581ffc9f0 authored over 5 years ago by Oliver Alka <[email protected]>
works great for yeast

c0791a00abcab27119b4bb39bfcc321aa25c5b4c authored over 5 years ago by kyowonjeong <[email protected]>
finished tests, need to reconsider implementation

ac94f57a23373acd383d8e6cafd90d288396d8f9 authored over 5 years ago by swew98 <[email protected]>
Merge pull request #4040 from hroest/feature/pyopenms_constants

[PYOPENMS] add physical and chemical constants

532890a6bec63fec3e61ea78601f3d4acc0cd464 authored over 5 years ago by Hannes Roest <[email protected]>
Merge pull request #4042 from OpenMS/nightly

Merge fix to Nightly

2602988a2a2892c664cc493ce0b983396baaf6b9 authored over 5 years ago by jpfeuffer <[email protected]>
Merge pull request #4041 from jpfeuffer/nightly

[FIX] move DPosition

2d4a898dc9ed3f30522dabd2b13e5d493edb1b89 authored over 5 years ago by Hannes Roest <[email protected]>
Merge pull request #4028 from timosachsenberg/feature/MzTab_lib

[FEATURE] move MzTabExport to lib and extend export

f14d2391bd3ed55d735fa4513265c647736ec7a6 authored over 5 years ago by Timo Sachsenberg <[email protected]>
Add note for unintuitive change

Co-Authored-By: jpfeuffer <[email protected]>

84f3b930ff6a3cc69fc41109b132b40837077a92 authored over 5 years ago by Hannes Roest <[email protected]>
Merge branch 'develop' of https://github.com/cbielow/OpenMS into develop

65776f2ce86072ef697a2ab633a6f8e434522483 authored over 5 years ago by TomW <[email protected]>
works great for yeast

0049fbef31129a4119d2063071ee9fe6ba0a543d authored over 5 years ago by kyowonjeong <[email protected]>
works great for yeast

e6f4f0570893945fdbd027eb697e991edc5228d9 authored over 5 years ago by kyowonjeong <[email protected]>
const msExp, testComute

1019aee7aa557dab2ecd5ec1dada754ced4b6d5c authored over 5 years ago by swew98 <[email protected]>
Merge pull request #37 from dominikschm/Contaminants

[FEATURE] Metric: Peptide Contaminants

d605adb90e287068e058f6b8d3e00ca1644f2d71 authored over 5 years ago by Chris Bielow <[email protected]>
Update Contaminants.cpp

c12c48fdcb9f73db430be1418cf5720d7bf65f6e authored over 5 years ago by Chris Bielow <[email protected]>
merged from develop cleared merge conflict

26a93396e7232432069e01a5303196bda7c1fa7e authored over 5 years ago by Dominik Sebastian Schmitz <[email protected]>
cleared merge conflict

372f22f80342565e1cc91e36f418f0d04459e89e authored over 5 years ago by Dominik Sebastian Schmitz <[email protected]>
changed the set hits in test

c5cfe83f7bb088cbaf11512503a5eba20d2b6aa6 authored over 5 years ago by Dominik Sebastian Schmitz <[email protected]>
added the third exception into the .h

b561fd3021e68270b62fdcbee3f8b6f1dd5bfdd0 authored over 5 years ago by Dominik Sebastian Schmitz <[email protected]>
specific, sensitive. Tol bug fixed

7c7803ee32aa2c5dc2542ffb3067ecc8bccf460a authored over 5 years ago by kyowonjeong <[email protected]>
specific, sensitive. Tol bug fixed

2ec6f0c7653e4e62dbc5152e395dfc823c43299c authored over 5 years ago by kyowonjeong <[email protected]>
[FIX] move DPosition

f2c10366418a7e0f46ed96d43ff4abe5b6509456 authored over 5 years ago by jpfeuffer <[email protected]>
Merge pull request #4014 from hroest/feature/pyopenms_meta

[PYOPENMS] fix inheritance for MetaInfoInterface / CVTermList

61791c34b562d00749b4a4f03b2ac299e108de3d authored over 5 years ago by Hannes Roest <[email protected]>
[PYOPENMS] add physical and chemical constants

e9d0881320e2a9bf248750fe1a37e8e88f24b61d authored over 5 years ago by Hannes Roest <[email protected]>
finished class.cpp so far, started with test implementation

e1857579d793471db9c2833ba1e439f1ed36562f authored over 5 years ago by swew98 <[email protected]>
[FIX] fix tests

752a40f395991d9288fc4d3fb68f06619e58368a authored over 5 years ago by Hannes Roest <[email protected]>
fixed the compare function

e7c1d56072cd96f884ee011d21ef690473b8bacd authored over 5 years ago by Dominik Sebastian Schmitz <[email protected]>
[FIX] (final fix)

8d1c1989e31b92a869558fa4a0aea00edaeca159 authored over 5 years ago by Hannes Roest <[email protected]>
Merge pull request #4031 from hroest/feature/isospec

Feature/isospec

6ba004f5a79cfc32603760e06dcbbbaa85bfc337 authored over 5 years ago by Timo Sachsenberg <[email protected]>
changed the code to iterate over all pepids instead of only looking at the first

5c1160b4c6b4eeda8dc18e035e3bc5a233c77f09 authored over 5 years ago by Dominik Sebastian Schmitz <[email protected]>
computation of ppm, changed result type, added metainfo

e9a63657ae8b5e1f5911917599a191351d01cf22 authored over 5 years ago by swew98 <[email protected]>
Update Contaminants.h

a73aa404a735d51158dca2e103f807a71f282425 authored over 5 years ago by Chris Bielow <[email protected]>
is_contaminant is now stored in pephits, computing with already digested database is now possible

dbbb6f2a38ae2c8ea432e44731db1439cf0ab402 authored over 5 years ago by Dominik Sebastian Schmitz <[email protected]>
Merge pull request #4035 from enetz/fix/xquest_parse_fdr

[FIX] OPXL: several fixes to xquest.xml parsing

61acbf36d68cec21a62719894d14fca0ebccd337 authored over 5 years ago by Eugen Netz <[email protected]>
First correction

fbc1021af423d3c65d84eb50552ed3c35cb4725a authored over 5 years ago by jschmacht <[email protected]>
Merge pull request #4038 from hendrikweisser/fix-nasg-proton

Addendum to PR #4020: use proton mass for charges

6df682c53f3b355a7ed9d0f909f05bb80603f8f4 authored over 5 years ago by Timo Sachsenberg <[email protected]>
[FIX] use proton instead of hydrogen mass for generating charged spectra of nucleic acids

82027eb7c41bb650b333420ef491c63ef15ac606 authored over 5 years ago by Hendrik Weisser <[email protected]>
Update ModificationsDB.cpp

54d4a11f237c932a3b7870294c86e578b878cf3e authored over 5 years ago by Hannes Roest <[email protected]>
Merge branch 'develop' into feature/aaseq_fixes

473cdf938f4e1aa4f5e7bc3c414a2faa7497faaf authored over 5 years ago by Hannes Roest <[email protected]>
Merge pull request #4027 from hendrikweisser/fix-formula-negative

Support negative charges in 'EmpiricalFormula::getAverageWeight' (fixes #1041)

903fc85a8687d73332ac6fb4aee0c24e071420fc authored over 5 years ago by Hannes Roest <[email protected]>
ms spectrum to peptideidentification

18a176da53230d4a95152fad3a8326062eb869b7 authored over 5 years ago by swew98 <[email protected]>
added a test to check if empty unassignedpeptideidentifications is valid

c98d3c01860da5b6163f76b4b15841670097ce80 authored over 5 years ago by Dominik Sebastian Schmitz <[email protected]>
[TEST] updated XFDR test files

I checked by sorting the old and new result files by score,
most of the difference comes from re...

97a53932cca38efdd297a84a53e29ab216dbe08c authored over 5 years ago by enetz <[email protected]>
[ADD] thirdparty test, refactor MetaboTargetedAssay

5ff6512b76e8f3a8c4313bf60530a672d548a878 authored over 5 years ago by oliveralka <[email protected]>
Theoritical spectrum

86056a49c5e1c77ec5a01bdb211ba41f526dfb1c authored over 5 years ago by swew98 <[email protected]>
added empty_features to output struct

aec73359f5337a0a9582b870ff47ec12912be225 authored over 5 years ago by Dominik Sebastian Schmitz <[email protected]>
isotope count scoring removed + isotope cosine automatic according to mass

1b98035d1aa59de2d558c881dc8147dd7cd6dd63 authored over 5 years ago by kyowonjeong <[email protected]>
isotope count scoring removed + isotope cosine automatic according to mass

d59d5ea5e4b56dec3d0dfe0c1296958048e34d4e authored over 5 years ago by kyowonjeong <[email protected]>
change documentation

9758f882ee0e8a7704eb244f72d88130d691d603 authored over 5 years ago by jschmacht <[email protected]>
isotope count scoring removed + isotope cosine automatic according to mass

d5e83fb32e6e0b029b0ca0675700443c70c9a5cf authored over 5 years ago by kyowonjeong <[email protected]>
[FIX] include fix

efa33d21c9a56d4e25c614c2d4972943eafed9de authored over 5 years ago by Hannes Roest <[email protected]>
change trafo to const

cb6d441f66a26ba9aafaaaa1124f2a6ce8f1a83d authored over 5 years ago by jschmacht <[email protected]>
[ADD] MID, FIX usw_known_unknows, add new tests

d088604fd55d1d90cf6d44cadcd9f34daec70cbb authored over 5 years ago by oliveralka <[email protected]>
Merge pull request #4033 from timosachsenberg/feature/modgen

[FEATURE] refactor ModPepGenerator and expose to pyOpenMS

f971b29d56a173e089310ac83cf9825a672909a8 authored over 5 years ago by Timo Sachsenberg <[email protected]>