github.com/OpenMS/Tutorials commits | Ecosyste.ms: OpenCollective

[FIX] figure ref

eba4e4024ca5b56079790404eee76995a767ea82 authored almost 5 years ago by oliveralka <[email protected]>

Fixed the port types in Metabolite ID

55e758418c8aae354d68f5cd3f5c22ba575ee6db authored almost 5 years ago by Julianus Pfeuffer <[email protected]>

Added dplyr to MSstats R nodes. USed rel. paths.

ea9d6bb89e5c4f9904f61317ea1fcc681ab9126d authored almost 5 years ago by Julianus Pfeuffer <[email protected]>

use vmargs

61fddf247fea6c24c24fc6f49d51db62a599e3bd authored almost 5 years ago by jpfeuffer <[email protected]>

modify tmp dir

2f2c1468c8839f237d8989ce22dd3a5eaafb8ccd authored almost 5 years ago by jpfeuffer <[email protected]>

minor fixes

df1a6d5a3049d7d00c3b751d6d6914eb716904c0 authored almost 5 years ago by oliveralka <[email protected]>

additional fixes

85deee4e3a45e856ae4038edf402f5d0fb1c1ffa authored almost 5 years ago by oliveralka <[email protected]>

Updated workflows with new OpenMS 2.5 parameters

OpenSWATH:
- multiple new params in the one OpenSWATH node

labelfree_with_protein_quantific...

931c001c82968c6d700a62ad557cbbe53349d519 authored almost 5 years ago by Eugen Netz <[email protected]>

test did not work

8cd1550d35ce910c7d091236f11308b0e98e7692 authored almost 5 years ago by Julianus Pfeuffer <[email protected]>

test

1392436f8e80e8670cedc19529d619599f2b0651 authored almost 5 years ago by Julianus Pfeuffer <[email protected]>

Had to switch from workspace relative to workflow relative bc in Batch mode, there is no workspace.

e604080e5c812009e67e1f2f13bfe461d9112ec6 authored almost 5 years ago by Julianus Pfeuffer <[email protected]>

Update basic pep id to use mountpoints

030ee5690c789febd0d1951c538b01d454f87c89 authored almost 5 years ago by Julianus Pfeuffer <[email protected]>

[ADD] In_design; MSstatsConverter; Check mapping by precursor

82a1056ba5e23517bb78fac739a81350623bf5d2 authored about 5 years ago by oliveralka <[email protected]>

[FIX] inital fixes

cac854a328cf1478d591b9eed208c3d39b32fe08 authored about 5 years ago by oliveralka <[email protected]>

[UPDATE] example data path, fixes mime tpye

8fa97d6b228858b87dc9ca8af3ccfdb78cbe888b authored over 5 years ago by oliveralka <[email protected]>

[FIX] metanode, FileMerger

575049d4d623b8cf82b9c1c936745ee568bdf776 authored over 5 years ago by oliveralka <[email protected]>

Workflow for isobaric analysis (untested)

Reduced rt setting in IDMapper
TMT6-plex (K,N-term) in MSGFPlus
The correction Matrix for the...

c664da60c13bd87b36d0ef0a3b9d4f30d2b93506 authored over 5 years ago by Oliver Alka <[email protected]>

Update runner script (only basic_ID workflow for now)

52cff6325442bc834fffb0a83cbcb5114e5f60ae authored over 5 years ago by jpfeuffer <[email protected]>

Merge pull request #164 from jpfeuffer/master

[Feature] Test Workflow-relative paths

930faebae86fafd4286619fff9bd3416d75e092f authored over 5 years ago by jpfeuffer <[email protected]>

Merge branch 'master' of https://github.com/OpenMS/Tutorials

1df6a425a366d90fb3ee4e032d7dbfc0a01321c1 authored over 5 years ago by Julianus Pfeuffer <[email protected]>

enable all

d0d90ae69c71ade6cacc2d4827624613b1e6bd87 authored over 5 years ago by timosachsenberg <[email protected]>

Update metabolomics.tex

849577bc610b4bd37de544c819376c17713a3d05 authored over 5 years ago by Timo Sachsenberg <[email protected]>

Update gettingstarted.tex

eb566925d3c3d4fca19d00013d48743d1b1cb2b4 authored over 5 years ago by Timo Sachsenberg <[email protected]>

Update gettingstarted.tex

3e73a241725ed319b463cbc4c3939ddd81ec0e7c authored over 5 years ago by Timo Sachsenberg <[email protected]>

Update gettingstarted.tex

a13b92a9956c346cfb5fe87bcca0b3de911cf67e authored over 5 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #155 from oliveralka/Boston2019

[Update] SiriusAdapter

1a2add43aca46bcd8988b1428fd2e9e5a92c266d authored over 5 years ago by Timo Sachsenberg <[email protected]>

[UPDATE] Metabolomics WF

78a7859e410f24932033b632fb8ec2be9a2e7d98 authored over 5 years ago by oliveralka <[email protected]>

[Update] SiriusAdapter

807c82e59aafcd208ba97de30701389154a48a7a authored over 5 years ago by oliveralka <[email protected]>

[FIX] remove swath from tutorial

745b8cd110a5a2d3dab0c063bdca6210a6985da5 authored over 5 years ago by timosachsenberg <[email protected]>

Updated basic_pep_id to workflow-relative paths.

3ec4b3dbb98a9082080c4d8927c6f74dc1819df6 authored almost 6 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #151 from oliveralka/EuBIC2019

[UPDATE] First changes EuBIC2019

93b925afd3828ee0c548e8883f9aad169d51465a authored almost 6 years ago by Timo Sachsenberg <[email protected]>

[FIX] absolute path and further changes

635a3656423206758a0b19cae5e8a9dd1b109bc6 authored almost 6 years ago by oliveralka <[email protected]>

[FIX] comment pyProphet installation instructions; additional smaller

changes

85df3663fea8d6ba254b15ee383efd3eb1fc7dd7 authored almost 6 years ago by oliveralka <[email protected]>

[FIX] KNIME, windows commands

8a41bce2f47ad317a582d231e7be5a3eb8c5ec8d authored about 6 years ago by oliveralka <[email protected]>

[ADD] changes style, dir structure

339f40efc253b1d817136a1e799da707b2e9c041 authored about 6 years ago by oliveralka <[email protected]>

[ADD] further changes

f812b590e86783a5964a128b4123c2bdb50fb237 authored about 6 years ago by oliveralka <[email protected]>

[FIX] pyopenms.tex

b08d47902e1acae491dbc7114c8a9c45da39d7e6 authored about 6 years ago by oliveralka <[email protected]>

[Tutorial]

34025ffd2bef100190c2e3785a4081209906cd2f authored about 6 years ago by oliveralka <[email protected]>

[UPDATE] First changes

cc3ef9bdd3df078535f8ff4f79f580c979b006a0 authored about 6 years ago by oliveralka <[email protected]>

Update myNotes.cls

add date & realign CC BY 4.0

e048963355c717f6d35df7e6ac869f4af2f277ec authored over 6 years ago by oliveralka <[email protected]>

Update myNotes.cls

introduce hard line break

759b93ec976301156d473e7951dd576b499af38c authored over 6 years ago by oliveralka <[email protected]>

Update myNotes.cls

next try

bb9f23b9ba0b35afd1f0aa63afa0b91816d8a91c authored over 6 years ago by oliveralka <[email protected]>

Update myNotes.cls

fix date

c44cc95c3f63eabe241f11df9e6c55895b949166 authored over 6 years ago by oliveralka <[email protected]>

Update myNotes.cls

add today

a516c20789fb3ff02973887d24b1cac31645d75d authored over 6 years ago by oliveralka <[email protected]>

Update myNotes.cls

try to add date

105ec51260a1c5602e807cf1d4aaa77f8975fab8 authored over 6 years ago by oliveralka <[email protected]>

Update metabolomics.tex (#149)

Fix for some visual in adduct grouping section

400db6d5b70b8aef8ec47c60ba860c521c1b2769 authored over 6 years ago by FabianAicheler <[email protected]>

[ADD] MAD (#147)

* [add] MAD description, Sirius fix

* [ADD] KNIME Workflow Metabolite_Adduct_Grouping

b55a629284e693838b9b54d3d0b02e5eec98299d authored over 6 years ago by oliveralka <[email protected]>

Update gettingstarted.tex (#148)

dbdac65657e54b7b02d0580530c6729230f87655 authored over 6 years ago by Timo Sachsenberg <[email protected]>

Feature/um2018 (#146)

* initialized default values for new parameters (#144)

to avoid warnings when loading these w...

49f9e94976945a092e3a07395a24749eaca18944 authored over 6 years ago by Timo Sachsenberg <[email protected]>

Further updates to metabo KNIME workflow pictures (#145)

8fd87debf4b96dcf60a1dc7bb7a2615036e16c2f authored over 6 years ago by Marc Rurik <[email protected]>

Small changes in R and some usages of OpenMS version

d6074af6df615abc3b23e3327268cce9f18dd739 authored over 6 years ago by Julianus Pfeuffer <[email protected]>

Remove old metabo KNIME workflow pictures

920d40bb7515f40d8f14633cb7218f0871b1b89a authored over 6 years ago by Marc Rurik <[email protected]>

Update metabo KNIME workflow pictures

1dbcee3bf6744b89cdc64a10fe0210abc613be88 authored over 6 years ago by Marc Rurik <[email protected]>

update msstats install instruction

7d95093281637a74a5d547cb97f6d9d6dce5ff72 authored over 6 years ago by Timo Sachsenberg <[email protected]>

[DRAFT] Add SiriusAdapter (metabolomics) (#139)

* [ADD] Update links install software KNIME

* [ADD] column header
[ADD] explain manual valid...

301383795c2b69a73347da8088c54fd2f5b59496 authored over 6 years ago by oliveralka <[email protected]>

Merge pull request #141 from oliveralka/update/MetabolomicsWF240

[Update] metabolomics workflows 2.4.0

38842eaeb6c8894c5b88856b710d85108b283db1 authored over 6 years ago by Timo Sachsenberg <[email protected]>

[ADD] update picture speclib

a8d27cb33b5c7b24ce3326530357ffdc35a93660 authored over 6 years ago by Oliver Alka <[email protected]>

Merge pull request #143 from jpfeuffer/fix/hotfix_underscores

Escape underscores

278256b0f1379940cc63a95b8706b827b372add6 authored over 6 years ago by jpfeuffer <[email protected]>

Escape underscores

0189fc9054526d27fdcf0887c931e9f3cb13614f authored over 6 years ago by Julianus Pfeuffer <[email protected]>

Fixes #118, #114, #111, #95, #66 (#142)

e779bc39e2a3a799c1e9030f18ed8ca4b2cd8965 authored over 6 years ago by jpfeuffer <[email protected]>

Updated proteomics WFs to 2.4 (#140)

* Updated proteomics WFs to 2.4

* Synced the MSStats WFs. Added a WIP execute batch file.

0e3067518ec306e4c7f25e57d7aa4ad21b81dc93 authored over 6 years ago by jpfeuffer <[email protected]>

Addresses #132

95faa528346c372cc87f55c3ebf0f698f0412060 authored over 6 years ago by jpfeuffer <[email protected]>

[UPDATE] SpecDB old SpectralID without database; add update 2.4.0; add

SiriusAdapter workflow
# Please enter the commit message for your changes. Lines starting

4d731ca0349ed4fa60cb93adbff9fc0aad3cecc1 authored over 6 years ago by Oliver Alka <[email protected]>

Merge remote-tracking branch 'upstreamd/master'

d6ac3cf9d4b64df8a22f91af72d079aee1ad4851 authored over 6 years ago by Oliver Alka <[email protected]>

Update KNIME update site

7c23632a2f135baa7dab971434842a579dcc3f74 authored over 6 years ago by jpfeuffer <[email protected]>

Update gettingstarted.tex

0a1411925854dd9f743b2bcd7e49b382d835fe26 authored over 6 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #135 from FabianAicheler/upstream/feature/Boston2018

add Proteomics megaworkflow; remove old subworkflows

2ebe1d397f3d662446e5ede7264f39be0e2cbc0f authored over 6 years ago by Timo Sachsenberg <[email protected]>

Merge remote-tracking branch 'upstream/master'

741d8a2ef9768734c0d7e4e59b335d880fc97f0d authored over 6 years ago by Oliver Alka <[email protected]>

Update labelfree.tex

0006b3516297283b33824034082d01289adb3b8b authored over 6 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #138 from OpenMS/feature/Boston2018

Feature/boston2018

c230de984378070dd2d206bb56a980e5b63ecdf4 authored over 6 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #137 from oliveralka/fix/Boston2018

[FIX] update figure 13 and ref

fba412827f9460223843ff881578c991555d8014 authored over 6 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #136 from Leon-Bichmann/fix/pwizard_image

Fix/pwizard image

099812b3fccb6debd37055b725c8fdbbc6bc7ea9 authored over 6 years ago by Timo Sachsenberg <[email protected]>

[FIX] update figure 13 and ref

742b3a311919dda1bac638c92f3c270a8c51a232 authored over 6 years ago by Oliver Alka <[email protected]>

pwizard_image

e6f885b990bdadc2290d57cb64e27107702c1764 authored over 6 years ago by Leon Bichmann <[email protected]>

pwizard_image

e55f223f6660d49115fbf1a9e8bfbd9de6cdaad4 authored over 6 years ago by Leon Bichmann <[email protected]>

add Proteomics megaworkflow; remove old subworkflows

e23c1c149862e80e82adcb3abdbc5367d5f35674 authored over 6 years ago by FabianAicheler <[email protected]>

[FIX] Small typo

ffbd68567133c3fbe152673fd10474c579c1b139 authored over 6 years ago by jpfeuffer <[email protected]>

Merge pull request #129 from FabianAicheler/Boston18stuff

Boston18stuff

83f556446ef71f1a1712be782dccdaaf901eb83d authored over 6 years ago by Timo Sachsenberg <[email protected]>

Merge branch 'feature/Boston2018' into Boston18stuff

a8b5faddfcad363e97b775cb3dc1fd810ec1a0f7 authored over 6 years ago by FabianAicheler <[email protected]>

small rewordings

5218ae66ca5326cdde598590a557c8facd2aeab6 authored over 6 years ago by FabianAicheler <[email protected]>

[FIX] IPRG (#128)

1f7a5aaf3e4e781f9f090ab6995369a1c8cf1b50 authored over 6 years ago by oliveralka <[email protected]>

small rewords iPRG Intro

98905a7f9fbf639bcc971a6240c0cef92b78a923 authored over 6 years ago by FabianAicheler <[email protected]>

Reworked plugin installation. Removed full installer links, rearranged, etc.

a0ea48668000ee31973b8981446af78384c908ff authored over 6 years ago by Julianus Pfeuffer <[email protected]>

Update labelfree.tex

fc7cc676ba197de1103451fad5ec7766fa3ab42f authored over 6 years ago by Timo Sachsenberg <[email protected]>

Update labelfree.tex

1f05850f98e64f0b93c3f81577fdd4cba643490b authored over 6 years ago by Timo Sachsenberg <[email protected]>

Update labelfree.tex

cc3f2117f607635824819899d031fc819a09de2d authored over 6 years ago by Timo Sachsenberg <[email protected]>

Update labelfree.tex

bcb45510548eeb0ad435487594a381fd2961e680 authored over 6 years ago by Timo Sachsenberg <[email protected]>

Update labelfree.tex

1c8aaa74b088ddce9544c48d1b6a3b97cfced54e authored over 6 years ago by Timo Sachsenberg <[email protected]>

Update gettingstarted.tex

c3ff4eac1ab1e0465af8a0ba0c1cfa5745cbc305 authored over 6 years ago by Timo Sachsenberg <[email protected]>

Update troubleshooting.tex

f4af977ac290413535f4558c361902b6454a2c73 authored over 6 years ago by Timo Sachsenberg <[email protected]>

Smaller changes on the tables

326ae7d6c70863feee52a40f3f16738b761fb909 authored over 6 years ago by lukaszimmermann <[email protected]>

Merge pull request #124 from oliveralka/feature/Boston2018

Draft for MSstats iPRG tutorial

29af0d7402a1e11f87dbdc663666926d2352f35c authored over 6 years ago by Timo Sachsenberg <[email protected]>

Merge remote-tracking branch 'upstream/feature/Boston2018' into feature/Boston2018

3d00c54908ec75e229175cb7f5013d87445ee70e authored over 6 years ago by lukaszimmermann <[email protected]>

very long nightly path needs more space -> deitemize (#126)

the abibuilder msstats feature path for KNIME needs so much space that the current solution does...

90f50c320ef41ffd6556c6b69965c2c214a91f1f authored over 6 years ago by FabianAicheler <[email protected]>

[ADD] Some more result description

f9792ef755c503096ce7a4ee066cb72a90d6a86a authored over 6 years ago by lukaszimmermann <[email protected]>

Replace MSstats R workflow figure with latest version

f5e4cc917ecd2617f71c60c2f8dba944c62c1704 authored over 6 years ago by lukaszimmermann <[email protected]>

Merge branch 'feature/Boston2018' of http://www.github.com/oliveralka/Tutorials into feature/Boston2018

f2a21f968c5e2832367ff873e05832399a296f8b authored over 6 years ago by lukaszimmermann <[email protected]>

Merge branch 'feature/Boston2018' of http://www.github.com/oliveralka/Tutorials into feature/Boston2018

0085b2a2e995a2bec637fa5bb05313783e1f3a43 authored over 6 years ago by lukaszimmermann <[email protected]>

TODOs and reference to the premade workflow.

c5e241e17b5d029694599fdfa12c959447477894 authored over 6 years ago by Julianus Pfeuffer <[email protected]>

[ADD] Group Comparison paragraph

940343c052c871acbf3eba8c04b302c02d7b425c authored over 6 years ago by lukaszimmermann <[email protected]>