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github.com/OpenMS/OpenMS

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

Merge pull request #6264 from vrossow/maxquant-output

[FEATURE] support initial msms.txt MaxQuant output

510595e4fffc27f8f9b5e593a19ed8c86677f7b6 authored about 2 years ago by Chris Bielow <[email protected]>
[feature] updated Modomics.tsv to include standard thiol bases.

7185e2b4609fee952d60f90e7aae6b9a6c2cf091 authored about 2 years ago by Samuel Wein <[email protected]>
Merge branch 'develop' into fix_doc22

0d69188e6ae6f1cbbcf6f90993b8eb3d1759ad4b authored about 2 years ago by Chris Bielow <[email protected]>
Merge branch 'fix_doc22' of https://github.com/cbielow/OpenMS into fix_doc22

ec6a1736b7e3f968b584c13ac6eaf3d889e5ad75 authored about 2 years ago by bielow <[email protected]>
prevent line breaks within words in blocks of <code>

c692da31063a3417bc55966743216b2fe49c71f6 authored about 2 years ago by bielow <[email protected]>
Merge pull request #6380 from jpfeuffer/upd/submodules

update submodules

1bfec7e92e91f3e5a8b58b902488f478909a2830 authored about 2 years ago by Julianus Pfeuffer <[email protected]>
update submodules

7b5e4491173e8a0aeecb3d9dc7f6f918e80f14c8 authored about 2 years ago by Julianus Pfeuffer <[email protected]>
Update FeatureFinderMetaboIdent.cpp

a0862065f6af5647a01331aeb58b7cb2dc3e64c9 authored about 2 years ago by Timo Sachsenberg <[email protected]>
Update FeatureFinderMetaboIdent.cpp

43753a9944ca98262918f4703b2557ffe2e9f9a8 authored about 2 years ago by Timo Sachsenberg <[email protected]>
Update FeatureFinderAlgorithmMetaboIdent.cpp

c26bf001445909d995a7525ad45a39fd8829ecb6 authored about 2 years ago by Timo Sachsenberg <[email protected]>
[fix] add override option for FeatureFinderMetaboIdent. Added printing of filename in FeatureFinderAlgorithmMetaboIdent in warning

c01096427094fcad9500328fbbf633ece7c00de9 authored about 2 years ago by Samuel Wein <[email protected]>
Merge branch 'develop' into feature/new_thiols

868b3c6939c03ab67f3272de6f3cfbef6020a7fa authored about 2 years ago by Timo Sachsenberg <[email protected]>
Merge branch 'develop' into fix_doc22

41eea7f66fcd784459b3c5d74fa3ec315368e1d3 authored about 2 years ago by Chris Bielow <[email protected]>
fix API docs

64eef4fd50650e9cad3fcec2a6586396d39f58ef authored about 2 years ago by bielow <[email protected]>
fix documention errors (links etc)

e952c043a81a575c16e7101c49691e053a70da44 authored about 2 years ago by bielow <[email protected]>
fix mangled output due to misaligned section

0e63535b614a98b4d7cb35408a844795fe97e7c3 authored about 2 years ago by bielow <[email protected]>
Merge pull request #6362 from OpenMS/jpfeuffer-patch-1

[FIX] only use TARGET_RUNTIME_DLLs on WIN32 otherwise its empty

032b6e59af17137a37ce40e93623e8564348b926 authored about 2 years ago by Julianus Pfeuffer <[email protected]>
[fix] added warning when trying to run FeatureFinderAlgorithmMetaboIdent with data that has no MS1 scans. Run function just returns input map in this case.

2e242f378915864a3b28b0680941fadd40b431e3 authored about 2 years ago by Samuel Wein <[email protected]>
remove section with same name in coding-conventions.doxygen

beeb249d88f9e1018c9f8a83c7430f8852f19366 authored about 2 years ago by bielow <[email protected]>
remove duplicate section

c9112da38565e08ad37885c0255e5b1d8c445bde authored about 2 years ago by bielow <[email protected]>
doxygen does not support <nobr>

d850a394935b2d78666ce78253e3daf94e7dd382 authored about 2 years ago by bielow <[email protected]>
Merge branch 'develop' of https://github.com/OpenMS/OpenMS into refact_toppview

# Conflicts:
# src/openms/include/OpenMS/KERNEL/DimMapper.h

4af56c07896a74c20a54e94a30fdf42f9d0dc678 authored about 2 years ago by bielow <[email protected]>
Merge branch 'develop' into fix/FFMI_segfault

8796a5e81b4f735f6abd187005daf44e7cee1756 authored about 2 years ago by Samuel Wein <[email protected]>
[fix] fix segfault when passing data with no MS1 scans

40c33ec25753a9879d7371dd58a6bea7e4685f3b authored about 2 years ago by Samuel Wein <[email protected]>
Merge branch 'develop' into maxquant-output

9f6d37bfacc8fa72c446b9e1b501dd742ae14a09 authored about 2 years ago by Chris Bielow <[email protected]>
Merge pull request #6370 from OpenMS/upd/WM5toGTE

[UPD] WM5 to GTE and include headers

e597d7950d4558d44951b2d20465660de6c15d88 authored about 2 years ago by Julianus Pfeuffer <[email protected]>
Merge branch 'develop' into maxquant-output

cd03c063ca18c39a644f4ba03cb52934b10ddf90 authored about 2 years ago by Chris Bielow <[email protected]>
add template to init list

61691d921b5c966edcfdeafb3254fd6b4214957c authored about 2 years ago by Julianus Pfeuffer <[email protected]>
Merge branch 'develop' into upd/WM5toGTE

a37e018bdd757a1a68c3c341981982a14bd1aae7 authored about 2 years ago by Julianus Pfeuffer <[email protected]>
Merge pull request #6371 from OpenMS/fix/glpkRealOptional

[Deps] make GLPK really optional

4cb1010d49a0e3c38afc45dbd20663bdea8e6c22 authored about 2 years ago by Julianus Pfeuffer <[email protected]>
Update cmake/cmake_findExternalLibs.cmake

09686e6ac61c01618129ae84504bf6832a50d824 authored about 2 years ago by Julianus Pfeuffer <[email protected]>
Merge branch 'develop' into upd/WM5toGTE

fd4242205cd40aa68aa4c1145e360d48597202d3 authored about 2 years ago by Julianus Pfeuffer <[email protected]>
Update CMakeLists.txt

17f7ce72dab4784ab571c621f9889c69710e55dd authored about 2 years ago by Julianus Pfeuffer <[email protected]>
Update cmake_findExternalLibs.cmake

ebabcc897dcfebd3116431a27d297ed9f69b7ba7 authored about 2 years ago by Julianus Pfeuffer <[email protected]>
[Deps] make GLPK really optional

c5f620d646b8ae10b14ba428d28540d1a76c9213 authored about 2 years ago by jpfeuffer <[email protected]>
[UPD] WM5 to GTE and include headers

8ba08da2e15d6b3f04446291f3f6778b80a176f1 authored about 2 years ago by jpfeuffer <[email protected]>
Merge branch 'develop' into fix-docstrings-2

1d852d2abc77215e3288ee8dda7ce6bb1073ce69 authored about 2 years ago by Rahul Agrawal <[email protected]>
fixing docstrings

8ab2517e4106782968cb8ba8881cf46fa5f6bd32 authored about 2 years ago by rahul799 <[email protected]>
Update .gitpod.Dockerfile

33c808614cde6fae086cfacb0403d3d8119cce7b authored about 2 years ago by Julianus Pfeuffer <[email protected]>
Create GitHub readable license file. (#6366)

2ca59aba1a8699f57dd9d5f31197bb8ccbd7efc4 authored about 2 years ago by Julianus Pfeuffer <[email protected]>
fix :returns

ccd3c96383a1e2a03240a53cd3a6f23e829da20c authored about 2 years ago by rahul799 <[email protected]>
limit original spec size. implmented well.

74cfe2dac0063764e73b86691af307bacee44ac2 authored about 2 years ago by kyowonjeong <[email protected]>
fix-2

b1f5417d5caf2223dcc06417c6bfc95099583cb6 authored about 2 years ago by rahul799 <[email protected]>
Removing "Parameter heading"

4c7246ffa2cd185f152470147626d0d7b6e5ab28 authored about 2 years ago by rahul799 <[email protected]>
limit original spec size.

Implementation should be redone.

53336c26e093cb534eebb63aff53e2917ae924e7 authored about 2 years ago by kyowonjeong <[email protected]>
TopPIC frag masses are sorted by qscore when their count exceeds 500

de830d5179d57dc60202c29207edc3370bcd133e authored about 2 years ago by kyowonjeong <[email protected]>
TopPIC frag masses are sorted by qscore when their count exceeds 500

b6ed18b3021acd019763225a816c62efa25fcadb authored about 2 years ago by kyowonjeong <[email protected]>
TopPIC frag masses are sorted by qscore when their count exceeds 500

64718a85c3c2ca68d7d4e0270f5564759e52d940 authored about 2 years ago by kyowonjeong <[email protected]>
TopPIC frag masses are sorted by qscore when their count exceeds 500

4775e234f1cac15b254eb51bafe02590c6740b81 authored about 2 years ago by kyowonjeong <[email protected]>
missing occurences

412a948f92c1340f29efbde98c48f4d4ea883f59 authored about 2 years ago by Julianus Pfeuffer <[email protected]>
underscores in cmake

986d39b0866785353f8a5f75689124fcf2e99eda authored about 2 years ago by Julianus Pfeuffer <[email protected]>
missing underscore

568ad8480e478c8d89576efd22af1b994a47e2be authored about 2 years ago by Julianus Pfeuffer <[email protected]>
TopPIC frag masses are sorted by qscore when their count exceeds 500

11214b8ca84cb9ce62d2ff3f612e2b4bb9d592f5 authored about 2 years ago by kyowonjeong <[email protected]>
[PYOPENMS] cleanup interfaces

228c6e9dc61f412d0a741a4880b500b4dd23e073 authored about 2 years ago by Julianus Pfeuffer <[email protected]>
only use TARGET_RUNTIME_DLLs on WIN32 otherwise its empty

a111ef58bc772e84e5b0a7bef4f0e57e2bb7d887 authored about 2 years ago by Julianus Pfeuffer <[email protected]>
Merge remote-tracking branch 'remote/fix-docstrings' into fix-docstrings

4272d40449bfceb47d6fac92d76a06fd20af4fea authored about 2 years ago by rahul799 <[email protected]>
fix

e2c0bc959e6a739204146bd5cf415034d5abbd1a authored about 2 years ago by rahul799 <[email protected]>
Parameters added

bf17c7eff28706463769c5a196eb133463d44a3b authored about 2 years ago by rahul799 <[email protected]>
Merge branch 'develop' into fix-docstrings

1ab7b7b0f2cfe596c849e26fa7ecb995fd5fc87a authored about 2 years ago by Rahul Agrawal <[email protected]>
Merge pull request #6360 from OpenMS/nightly

Update pyopenms-wheels.yml

e1aed809e067e6ffc4cae2b7988eb2fff7ccb8f3 authored about 2 years ago by Samuel Wein <[email protected]>
fixing docstrings

4c358697714ed57b356c9c7c727971aa2865405b authored about 2 years ago by rahul799 <[email protected]>
Update pyopenms-wheels.yml

[fix] fix nightly repo url

531cea668655fddacf9559656f12f80171a8a255 authored about 2 years ago by Samuel Wein <[email protected]>
[Feature] MetaboliteSpectralMatcher optional spectra merging and export of native spectrum IDs (#6349)

* MSM parameter for optional merging of spectra

* add optional output of merged spectra as mz...

d3863c4dbbe9b873ab98408dd14b58a0f89baa7a authored about 2 years ago by axelwalter <[email protected]>
TopPIC frag masses are sorted by qscore when their count exceeds 500

e27101065c23cfc9c542a5b9e7b932aae9f4b9fa authored about 2 years ago by kyowonjeong <[email protected]>
TopPIC frag masses are sorted by qscore when their count exceeds 500

070a2356654c21634c51890c8a10920f94866bdd authored about 2 years ago by kyowonjeong <[email protected]>
[FIX]: QBytesArray::append(QString) is deprecated (#6101)

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

9f26f3e0ea84fdd382d50adeb5a2f50dafbc430b authored about 2 years ago by AMIT KUMAR MISHRA <[email protected]>
Merge pull request #6354 from OpenMS/jpfeuffer-patch-1

Upload to nightly pypi repo

c205ebc28cce6af72a240165918118f39166b2b6 authored about 2 years ago by Julianus Pfeuffer <[email protected]>
Upload to nightly pypi repo

9c4629c00622de005d2e62ee7f9c9872434dbced authored about 2 years ago by Julianus Pfeuffer <[email protected]>
Merge pull request #6353 from OpenMS/jpfeuffer-patch-1

[FIX] adapt tests to changes in ExperimentalDesign Sample numbering

33159470824b047f955b506c52d7001c22f29242 authored about 2 years ago by Julianus Pfeuffer <[email protected]>
adapt tests to changes in ExperimentalDesign Sample numbering

f35b3463f1550f6a51c3cec12cee850cb2e4dba2 authored about 2 years ago by Julianus Pfeuffer <[email protected]>
TopPIC frag masses are sorted by qscore when their count exceeds 500

3c63e8e770ed4d4cb3a790ccfbee0840c67e304a authored about 2 years ago by kyowonjeong <[email protected]>
Merge pull request #6316 from OpenMS/jpfeuffer-patch-4

Move install location of thirdparty headers into openms include dir

db7eb01d0bdf0594de202c66f25ca22d3fc71f0a authored about 2 years ago by Julianus Pfeuffer <[email protected]>
TopPIC frag masses are sorted by qscore when their count exceeds 500

4c593e9148b157b21bbb10750768acb9cd0304dd authored about 2 years ago by kyowonjeong <[email protected]>
TopPIC frag masses are sorted by qscore when their count exceeds 500

4cdad281341d9429ab953be46bfb6d7d11620dd3 authored about 2 years ago by kyowonjeong <[email protected]>
TopPIC frag masses are sorted by qscore when their count exceeds 500

baa0f864a001d48b2d0b4e776242a4086c3da63a authored about 2 years ago by kyowonjeong <[email protected]>
Merge pull request #6350 from OpenMS/nightly

Update gh-action-pypi-publish

a581f6c3d7a21cb8ccca64fcbf516c29838fad82 authored about 2 years ago by Samuel Wein <[email protected]>
Update gh-action-pypi-publish

master tag is deprecated, migrating to release/v1 as suggested on https://github.com/pypa/gh-act...

e161f3f9474789a95fee4a44268661490d608f5a authored about 2 years ago by Samuel Wein <[email protected]>
Merge pull request #6348 from OpenMS/wheels-macos-fix

Update pyopenms-wheels.yml

9864d5c4804a46a17cdd22d85d4ce0ace4e251a6 authored about 2 years ago by Samuel Wein <[email protected]>
Update pyopenms-wheels.yml

Bump version of cmake for build-macos

304f80663699f1289fe7925a12b85dd02bc607ba authored about 2 years ago by Samuel Wein <[email protected]>
Merge pull request #6347 from OpenMS/fix/mztab_exp

workaround for MzTabExporter not being able to export ids with empty …

05bc770ba8fda94e0341a1cd35d00b5607fbe976 authored about 2 years ago by Timo Sachsenberg <[email protected]>
workaround for MzTabExporter not being able to export ids with empty hits

4adfc5250538c8d2a107b10386eaf2a51a38bc07 authored about 2 years ago by Timo Sachsenberg <[email protected]>
Masstrace isotope bug fixed

70ed07f1e9833d43337c8af4d87ae2ed8ec9f70b authored about 2 years ago by kyowonjeong <[email protected]>
bug fixing - not udpated files from origin/feature/FLASHDeconv

cc8f125e141fe86f2bd73e0327383592cdcaafd6 authored about 2 years ago by JeeH-K <[email protected]>
bug fixing - not udpated files from origin/feature/FLASHDeconv

dae16ad99369945d5c6658db1f9e99443cbdd630 authored about 2 years ago by JeeH-K <[email protected]>
Merge remote-tracking branch 'origin/feature/FLASHDeconv' into feature/FLASHDeconvOnly

e4d0f9185aad98d727cf3f9f27bc7620fe4d5178 authored about 2 years ago by JeeH-K <[email protected]>
Merge remote-tracking branch 'upstream/develop' into feature/FLASHDeconvOnly

feb01de613d3aadfc8de6bb62bedf3524488dff5 authored about 2 years ago by JeeH-K <[email protected]>
Merge remote-tracking branch 'upstream/develop' into feature/FLASHDeconv

2e8e220a680a39a232f5e074a2518b8751af76f2 authored about 2 years ago by JeeH-K <[email protected]>
Masstrace isotope bug fixed

3dc8d62105cb6960cd6e42e065a92d5f6b6ba829 authored about 2 years ago by kyowonjeong <[email protected]>
Merge pull request #6284 from OpenMS/feature/MSP_spectral_matching

[Feature] MetaboliteSpectralMatcher input databases in msp and mgf file format

a0b4326b7e2ed868f48a310f89ede6bb556cd659 authored about 2 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #6344 from OpenMS/fix_scoregetter

correct parameters

14ef63f24f8781c8e54425828de256a0cad733cd authored about 2 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #6343 from OpenMS/remove_qtconcurrent

remove dependency to QtConcurrent

1f511f0ecb14d44855e26e75983e1e410d2e1b4d authored about 2 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #6345 from OpenMS/fix_pyopenms

fix pyOpenMS wrapping of ExperimentalDesign

d4ae8bde64597b45f24170f4d4c4ba51369ac2ff authored about 2 years ago by Timo Sachsenberg <[email protected]>
fix pyOpenMS wrapping of ExperimentalDesign

1cba615dec175d2798000d204125b9afcbfba23c authored about 2 years ago by Timo Sachsenberg <[email protected]>
Update TOPPASOutputFileListVertex.cpp

32723d8f43278893e79c1a05eed9e1ea8c0f0046 authored about 2 years ago by Timo Sachsenberg <[email protected]>
Merge branch 'develop' into feature/MSP_spectral_matching

4f81379514e12a2cdd3acd566095a02538a57fd9 authored about 2 years ago by Timo Sachsenberg <[email protected]>
correct parameters

e53ef6d4a9ee651352c2c8b0dd63559d083beed5 authored about 2 years ago by Timo Sachsenberg <[email protected]>
remove dependency to QtConcurrent

b4bd33dce50b5d292f340bbd00b0ccf1fdd041dc authored about 2 years ago by Timo Sachsenberg <[email protected]>
Merge branch 'develop' into feature/nase_debug

91a23c146e5ebd3c31c0d74c48dae01510c2d886 authored about 2 years ago by Samuel Wein <[email protected]>
[fix] fix merging of NASequence thiol code

121f93755231b953d5bd3ac9951ca310bc16bdcf authored about 2 years ago by Samuel Wein <[email protected]>
Merge branch 'feature/new_thiols' of ssh://github.com/poshul/OpenMS into feature/new_thiols

39edffac7ab94f2ebdd704233b3ed97ef83923ad authored about 2 years ago by Samuel Wein <[email protected]>