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

peak isotope index offset error fixed..

c8bf60cd9946d07f226004c7b320a9ed924dd2f7 authored about 5 years ago by kyowonjeong <[email protected]>
All warnings have been resolved.

35f0b47cfeb7ec1bd3843740d8057b78a541bad5 authored about 5 years ago by kyowonjeong <[email protected]>
directory mzml file read implemented

72fa84b19a75106ea75436405172ca1e323c0434 authored about 5 years ago by kyowonjeong <[email protected]>
cleaned up

b1c2d5ad3a29c00ea3715788e156db553f22fb8e authored about 5 years ago by kyowonjeong <[email protected]>
directory mzml file read implemented

4820d47169fb8274e597185811aa1318caf6e192 authored about 5 years ago by kyowonjeong <[email protected]>
directory mzml file read implemented

3e2b96370eac6afc315023a957edfdac245444a4 authored about 5 years ago by kyowonjeong <[email protected]>
directory mzml file read implemented

bc70b00d268b9918e62849f6e2602d4f3f0405b3 authored about 5 years ago by kyowonjeong <[email protected]>
directory mzml file read implemented

6b19e90be85449cbf3bef42b83628c0d82f50b17 authored about 5 years ago by kyowonjeong <[email protected]>
MzBit wrong access bug fixed.

513d4c1ad89465173d1d82244cf85eba0c291bee authored about 5 years ago by kyowonjeong <[email protected]>
MzBit wrong access bug fixed.

c91f96f36244d89cd6d1e107a2655933af598649 authored about 5 years ago by kyowonjeong <[email protected]>
Enable to get input file as directory

8fae1cefc2c4a1e397900d1330775b1fbf18e23d authored about 5 years ago by JeeK <[email protected]>
Output file formatting complete. Random output due to wrong vector reserve resolved

3994d7a8ec9f5cfe3d95706ab4b69f12f33da8d1 authored about 5 years ago by kyowonjeong <[email protected]>
MzBit wrong access bug fixed.

368330e613d912d1509fe1bb33a067d024cdd04a authored about 5 years ago by kyowonjeong <[email protected]>
merged with option selectin. renamed to flahsdeconv

fc00d4c3445849f031b8876e7e6da28502a3bced authored about 5 years ago by kyowonjeong <[email protected]>
Changes for completing test

8c31ae471b4cbe25fd679c62feb4774defd7f1c1 authored about 5 years ago by JeeK <[email protected]>
Output file formatting complete. Random output due to wrong vector reserve resolved

d82e59de03bac79d708d8b9a4345c24bdcd46665 authored about 5 years ago by kyowonjeong <[email protected]>
Adding user options

882b4dd7f54ed753f53530f2286455b6d5274090 authored about 5 years ago by JeeK <[email protected]>
merged with option selectin. renamed to flahsdeconv

55533e0fa5abf45403810123c8c3d7b3dd258aa7 authored about 5 years ago by kyowonjeong <[email protected]>
Adding user options

507861f5ba5d1fbb5e6325e7b27f5b0f1c2f6e25 authored about 5 years ago by JeeK <[email protected]>
merged with option selectin. renamed to flahsdeconv

c126daae24df2793cbe3673a4abdbf892cb0d76b authored about 5 years ago by kyowonjeong <[email protected]>
souce code rearranged..

950282ecce68490a42893b30a81ebc351178dd9d authored about 5 years ago by kyowonjeong <[email protected]>
including usage options

43f9a9140a0619fc80f56e5908ab7713a3e7a755 authored about 5 years ago by JeeK <[email protected]>
souce code rearranged..

347e60afe6711d3aaad217730ac88237cb7392a5 authored about 5 years ago by kyowonjeong <[email protected]>
ASMS2019. Deisotope improved - more focused monoisotope.

da3bcae4a225b4ff9d1f65935219b8bd157806db authored about 5 years ago by kyowonjeong <[email protected]>
ASMS2019. Deisotope improved - more focused monoisotope.

543aa096d53b39a17c2bb63f7cbddc9195487534 authored about 5 years ago by kyowonjeong <[email protected]>
souce code rearranged..

5cad58fcdefee5f5f3c289ce9f490da221987bbd authored about 5 years ago by kyowonjeong <[email protected]>
ASMS2019 version2 ... will be added for a few days..

df044edeafa689a752365c07c76df0b97f6007e2 authored about 5 years ago by kyowonjeong <[email protected]>
ASMS2019 version3 Isotope bug fixed and increased running time. ... will be added for a few days..

84bf87fd0895eda81259da502a35a63cc4669b4e authored about 5 years ago by kyowonjeong <[email protected]>
ASMS2019 version

daafa79ec7b988b2b38652b5499580f86657bd17 authored about 5 years ago by kyowonjeong <[email protected]>
isotope peak redundancy reduced..

dcd27747d2788f02c8bc2acc10c7a00782eeae65 authored about 5 years ago by kyowonjeong <[email protected]>
isotope peak redundancy reduced..

505cd7d622c9deb121c10b5308d4aa5159b4d28a authored about 5 years ago by kyowonjeong <[email protected]>
retention time output added

f34d859b109ef84c3597a93982374b349379f80b authored about 5 years ago by kyowonjeong <[email protected]>
Lower filtration thresholds and source code clean up (make some functions..)

da637ee4b046769c1e8d93ee6a8d90bf8db52a34 authored about 5 years ago by kyowonjeong <[email protected]>
fast, sensitive, specific.

Issues to address : peak redundancy for scoring, better scoring, isotope part..

aa5e606df6cc5457541af7290b1839c3b9b1f8cc authored about 5 years ago by kyowonjeong <[email protected]>
score threshold bug fixed..

50f5cb3504c280a94f6108dd110c473a02d8cafb authored about 5 years ago by kyowonjeong <[email protected]>
isotope grouping done isotope scoring is not done...

5bc585902d15bc7d0b66baa32f6f6857b9438084 authored about 5 years ago by kyowonjeong <[email protected]>
score threshold bug fixed..

39105ea2c49d4cb3f1ac9ce7475911cc533db91b authored about 5 years ago by kyowonjeong <[email protected]>
isotope basic filtering enabled.

Isotope env grouping is to be done.

f4abb1d29b1c3fecb85ed287f93471b724a3c73f authored about 5 years ago by kyowonjeong <[email protected]>
No sorting 5000 intensity filtering, even faster - yeast per spec 1.5msec, less stringent parameters...

21349ebfcf0833bbe86c8f92e4a66986d6a48dfc authored about 5 years ago by kyowonjeong <[email protected]>
No sorting 5000 intensity filtering, very fast - yeast per spec 2msec

6d797e9a812260f12f9e5b5eb37c9a170e50102f authored about 5 years ago by kyowonjeong <[email protected]>
No sorting 5000 intensity filtering, even faster - yeast per spec 1.5msec

3ec7b96d9b12dc510d9c53af173e89012fac182d authored about 5 years ago by kyowonjeong <[email protected]>
filterSpectrum implemented but takes too long (>3msec per spec)

2b4f9c285c26ee9f6bdd72e714b1bd026347e05d authored about 5 years ago by kyowonjeong <[email protected]>
In the middle of filterSpectrum implementation...

05249298040844316cf1fbb96dd293aad626d5e7 authored about 5 years ago by kyowonjeong <[email protected]>
simple log likelihood ratio scoring function implemented.

Tested with CytoC, Myo and works well.

72f53b146c1d54953eb1780e197f25062ce1d85f authored about 5 years ago by kyowonjeong <[email protected]>
simple log likelihood ratio scoring function implemented.

Tested with CytoC, Myo and works well.

87aa3bb52b51b5c42f2c4ae7d63abaad55228940 authored about 5 years ago by kyowonjeong <[email protected]>
Add LogMzPeak struct

43b4c2ebf3abaf58dc27511af0fb8ee46a63225f authored about 5 years ago by JeeK <[email protected]>
simple log likelihood ratio scoring function implemented.

Tested with CytoC, Myo and works well.

3c390eff1642186cc10eeb4e0b963364ce2ddd33 authored about 5 years ago by kyowonjeong <[email protected]>
a little bit change

399e4b90fa2d27b8c9433f9dca04d55e23c65acb authored about 5 years ago by kyowonjeong <[email protected]>
yeast dataset per spec 1.88msec

a39fe1c4401f383dfc3e755de246ba8695573ec2 authored about 5 years ago by kyowonjeong <[email protected]>
mass trace test parameter testing

942ebafc2ef36bedf7a576c90d511c97f163fe1a authored about 5 years ago by kyowonjeong <[email protected]>
mass trace test parameter testing

f0c5a6e7284754b155daac351a50cd2d5cf7cede authored about 5 years ago by kyowonjeong <[email protected]>
Add sorting

e17cc037ab8c109ce159b67bce3876c22e6e2e99 authored about 5 years ago by JeeK <[email protected]>
Add TopDownOnlineDeconvolution class

0da7a604d98b6ac8fc036c1a8612d4953f80efbb authored about 5 years ago by JeeK <[email protected]>
generate elution peak clusters - in progress

- collect close apexes : done
- clustering : in progress

b7bbe9204dc574af53e217bfacdc14f723e3e4ff authored about 5 years ago by JeeK <[email protected]>
generate interval - in progress

eb7263684fcb5b7acdeca471c0d0f7bf4cd532ea authored about 5 years ago by JeeK <[email protected]>
mass trace test parameter testing

c6d59ce444bc3b9b7fe01ae74fded5827bde8b8c authored about 5 years ago by kyowonjeong <[email protected]>
generate interval - in progress

- detect apexes : done
- sortng with RT : in progress

43437e15b098472676546a03125f000bf9d03164 authored about 5 years ago by JeeK <[email protected]>
mass trace test modified

421b56b775a1e092087201cf3eb97f1cd160f3ed authored about 5 years ago by kyowonjeong <[email protected]>
mass trace test added

22b15a12380a7a19f4262eb66a1e134e6f6338b0 authored about 5 years ago by kyowonjeong <[email protected]>
commit tests for new branch, feature/TDdeconv.

29f18887dac3652604b257bf58df71cbc99560a7 authored about 5 years ago by JeeK <[email protected]>
[NOP] add author

d9993265a5a9cf4e411f003c22cf80e63f2fa652 authored about 5 years ago by Kyowon Jeong <[email protected]>
commit tests for new branch, feature/TDdeconv.

601d96214915b53fb19cbb0e3d2d2c9c9aeb9359 authored about 5 years ago by JeeK <[email protected]>
Merge pull request #4225 from hroest/feature/protein-terminal

[FEATURE] handle protein N/C terminal modifications

a5903f78752457d371d499ce6b9342ff83ef88cd authored about 5 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #4233 from OpenMS/feature/osw_mod

Feature/osw mod

ddb44934ca982f1fbbf1620e764123bc06a0b5c6 authored about 5 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #4236 from hroest/feature/sort_toppview

Q: Why are we sorting all spectra in TOPPView?

6781acef29f0a01cd04b4926155ac4d3ca04acf1 authored about 5 years ago by Hannes Roest <[email protected]>
[TEST] add test

da6d84186cd1d852975214743f65bae32be5f368 authored about 5 years ago by Hannes Roest <[email protected]>
Update Spectrum1DCanvas.cpp

63ee50d31182080e5480b8128e8bd00dcc83d3d0 authored about 5 years ago by Hannes Roest <[email protected]>
Merge pull request #4238 from hroest/feature/build-fix

[FIX] use VersionInfo instead of Macro

6781f9eb316f2af8968153a7c3eb5e5db7aa4a51 authored about 5 years ago by Hannes Roest <[email protected]>
[FIX] fix for Skyline notation

2ab538b0f020c1c5d276a0de9b103835a3f0dae9 authored about 5 years ago by Hannes Roest <[email protected]>
Merge branch 'develop' into feature/osw_cleanup

de914d5768b3bead343df3761390ec51e9746e0d authored about 5 years ago by Hannes Roest <[email protected]>
Merge pull request #4237 from cbielow/fix_MSGF

[FIX] detect MSGF+ crash

e3de70dfdee1c014d9a0fb95fc05601fcc0566b3 authored about 5 years ago by Hannes Roest <[email protected]>
[FIX] use is_sorted

9259c6ad4f51c4496c5d7edcc1deb36ddb8eb481 authored about 5 years ago by Hannes Roest <[email protected]>
[FIX] use VersionInfo instead of Macro

3a55d92aa27f3de077d1be7b1e45bca08dc97bee authored about 5 years ago by Hannes Roest <[email protected]>
[FIX] detect MSGF+ crash when it wrongly returned exit code 0 upon failure

e496920d7563e5058dd264a53e8e70f7f5a0603f authored about 5 years ago by Chris Bielow <[email protected]>
[FIX] MSGF+ adapter fix (crash on mzML.gz input without error message)

f93545f1648e55425a0c77f4d0032a43fa094891 authored about 5 years ago by Chris Bielow <[email protected]>
[DOC] minor internal

2aa74fd1cc19459817e9514eada0bd82915e127c authored about 5 years ago by Chris Bielow <[email protected]>
[FIX] check for sorted container before sorting

25fe34b159af8f9bed2b5af98d5afe693605a191 authored about 5 years ago by Hannes Roest <[email protected]>
[FIX] add sorting again

da3fd144baa3faf119a919436a96d0fa92422079 authored about 5 years ago by Hannes Roest <[email protected]>
[FIX] no more sorting of all spectra for each new layer

bbd7f108ba30c3f1f892a3e6f91696ff6a5f0a48 authored about 5 years ago by Hannes Roest <[email protected]>
[TEST] change test files

28982ff63727618b4d5927c4298c914c40584c3e authored about 5 years ago by Hannes Roest <[email protected]>
[FEATURE] FFid with custom mods

b04861c5cd9cad8ccaa85351cec7a94d786850e9 authored about 5 years ago by Hannes Roest <[email protected]>
[TEST] update test

21ceb040ecbe81e6d6fc79aa9349b4c71e7a8f5a authored about 5 years ago by Hannes Roest <[email protected]>
[FIX] read also sequences that do not map to UniMod

7627d983e89ae9cbef0b9d264879110d11549026 authored about 5 years ago by Hannes Roest <[email protected]>
Update AASequence.cpp

4e268614f9062f1991d2dfac0d0397a1b2eb0ba6 authored about 5 years ago by Hannes Roest <[email protected]>
Merge pull request #4223 from jpfeuffer/fix/XtandemReadParams

[Fix] reading of optional parameter groups in XTandem output files.

0f1e2b8fd0ae8274e606a16890ee754fa24c22b6 authored about 5 years ago by Hannes Roest <[email protected]>
Until sth good is implemented for checking IDPEP fit, dont throw warning

cf8154da930d84ca3d6e6eb1fd3f0dbdfdbe13c2 authored about 5 years ago by jpfeuffer <[email protected]>
Introduced a stack for nested groups.

Signed-off-by: Julianus Pfeuffer <[email protected]>

d29d97b426b028d959c6ba59a85d00833b148583 authored about 5 years ago by Julianus Pfeuffer <[email protected]>
[NOP] remove newline

efd12420184b83c8ef915137940a44c5de97be67 authored about 5 years ago by jpfeuffer <[email protected]>
[FIX] deal with boolean values (#4224)

- improve conversion from text to boolean values
- ensure that Skyline output can be parsed dir...

5729daf92fed4c8eb86c117e54a2a0f5a1856b92 authored about 5 years ago by Hannes Roest <[email protected]>
[FEATURE] handle protein N/C terminal modifications

- properly parse protein C and N terminal modifications on amino acids
- allow protein C and N t...

e22197cda393053d9f651feb89e5d23c68fb8e88 authored about 5 years ago by Hannes Roest <[email protected]>
Merge pull request #4221 from jpfeuffer/fix/isobaricMzTab

[FIX] More fixes to correctly export more complex labelled experimental designs to mzTab

a5f2434e275c83be81a6774bfef8a1d3136ce182 authored about 5 years ago by Hannes Roest <[email protected]>
Fix reading of optional parameter groups in

XTandem output files.

Signed-off-by: Julianus Pfeuffer <[email protected]>

1c29aa974b041833202a22d2ba33d74594503f39 authored about 5 years ago by Julianus Pfeuffer <[email protected]>
Update ConsensusMap.cpp

8c6832df99ce4ec3031e980f6a4e03a9d0956941 authored about 5 years ago by jpfeuffer <[email protected]>
Updated affected ProteomicsLFQ test.

Signed-off-by: Julianus Pfeuffer <[email protected]>

58d119a591836ab315a1988e2f891ceffd779926 authored about 5 years ago by Julianus Pfeuffer <[email protected]>
Fixed bug in FileMerger that did not keep metavalues and

UIDs of features.

Signed-off-by: Julianus Pfeuffer <[email protected]>

67f235f0c1279d85499a7ca3b8b331ae35aefa1e authored about 5 years ago by Julianus Pfeuffer <[email protected]>
Fixed bug in FileMerger that did not keep metavalues and

UIDs of features.

Signed-off-by: Julianus Pfeuffer <[email protected]>

7849fa6696caf58e0dd273b4662bd3935e3ca8ee authored about 5 years ago by Julianus Pfeuffer <[email protected]>
More fixes to correctly export more complex labelled

experimental designs to mzTab.

Signed-off-by: Julianus Pfeuffer <[email protected]>

bf43ab93dea26d3b7b07ef1c7e67d3b5fe4ecb7a authored about 5 years ago by Julianus Pfeuffer <[email protected]>
[FEATURE] added Python bindings for meta value getters with defaults

f4a71586e8549514c05b241745bbd8902db1665e authored about 5 years ago by Hendrik Weisser <[email protected]>
[FIX] docu fix

8b648559ba55b167af6dce0f8dd5798881514421 authored about 5 years ago by Hannes Roest <[email protected]>
Merge pull request #4218 from jpfeuffer/tests/MS3

[Tests] interleaved ms3

d77f74ad148ed2928b74d32bc96907ed282fda50 authored about 5 years ago by jpfeuffer <[email protected]>