Ecosyste.ms: OpenCollective

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

github.com/OpenMS/Tutorials

Tutorials as used in the user meetings. (Please assign a git tag for the revision used for the UM)
https://github.com/OpenMS/Tutorials

Update README.MD

6da32b03b7b6c3f7e15831f4d1188e0890a16200 authored 10 months ago by Samuel Wein <[email protected]>
Added missing workflows. Updated existing workflows to not use deprecated nodes (for the most part)

e88af2e354bb92d0bf14230846fb75cc0db488b6 authored 10 months ago by Samuel Wein <[email protected]>
Update executeBatch.sh

032167798e3918e1e791b8e004feaf13d4c604db authored over 1 year ago by Julianus Pfeuffer <[email protected]>
Fixed OpenSwathWorkflow node settings

2eff627c4d552b9dea1644db19b31b388d38b940 authored over 1 year ago by Eugen Netz <[email protected]>
Fixed workflow paths and added Win batch script

d76a38ff956e99db931f04c355c0bdad66470b2d authored over 1 year ago by Eugen Netz <[email protected]>
Merge branch 'master' of https://github.com/OpenMS/Tutorials

810f6d470ace9c56f84e01064ef610de0f54ad35 authored over 1 year ago by Eugen Netz <[email protected]>
Updated workflow parameters and IO paths

ae7a76b177a8c330241c83da86ab5722cf2ce901 authored over 1 year ago by Eugen Netz <[email protected]>
Delete duplicate workflow

af1556b86423bc8df7d5c05502ac7f7eb5457ef4 authored over 1 year ago by Eugen Netz <[email protected]>
Cleaned up duplicate workflows

7a11e2bd4e799daa7227d85900ef1a942112c987 authored over 1 year ago by Eugen Netz <[email protected]>
Updated workflows to new OpenMS plugin structure

KNIME version: 4.7.1
OpenMS plugin version: 3.0.0.202305031152 (nightly)

Used the new File I...

ea10b90b798c05e9c447800776e511e2f274d59b authored over 1 year ago by Eugen Netz <[email protected]>
updated versions for Python, OpenMS and numpy

52f9d1b69c7f9743fb8a5786924a96342bcef1dd authored over 3 years ago by Samuel Wein <[email protected]>
Added ID with protein inference and spectral counting in protein quantifier

a78bb45cca50346c4608d5fa94fd216deba9fe1e authored over 3 years ago by Timo Sachsenberg <[email protected]>
[UPDATE] Metabolite_DeNovoID (#203)

169b37cd699a17d0d6842dca41dacba0d43da4a3 authored over 3 years ago by Oliver Alka <[email protected]>
Updated workflows for OpenMS 2.7 (#200)

6126da67112f2469bc14062bbe65104eaaae3d1a authored over 3 years ago by Oliver Alka <[email protected]>
Updated QC workflows for OpenMS 2.7

8026b12b7f06faad82a10eab88fa3bb6c5b9c945 authored over 3 years ago by Eugen Netz <[email protected]>
Updated OpenSWATH workflow for OpenMS 2.7

4bc855f42717204ed8d69faaa255f03eee9d25a1 authored over 3 years ago by Eugen Netz <[email protected]>
Delete OpenSwath.knwf

ae0b13e4d492216e8061cb6f0f4c39a1f0108a55 authored over 3 years ago by Eugen Netz <[email protected]>
Updated a few workflows for OpenMS 2.7

The node combinations of 'TextExporter -> IDTextReader' and 'TextExporter -> ConsensusTextReader...

02e490df704d06b8ef117830ff245d6b8dc0c10b authored over 3 years ago by Eugen Netz <[email protected]>
code (#195)

21426b879bcfabebb6bd38f5b5ec173f99e64d95 authored over 3 years ago by Oliver Alka <[email protected]>
[FIX] OSW Metabolomics (#193)

* Fix minted

a9fc7832de6c58e38860858b347a3ba4f41bc117 authored over 3 years ago by Oliver Alka <[email protected]>
OpenMS 2.7: Update WF related to Sirius (#187)

*ADD DIAMetAlyzer 2.0; Sirius 4.9.0; OpenMS 2.7

1280633edde8ddfd28cd22dace24517586d100d9 authored over 3 years ago by Oliver Alka <[email protected]>
Updated a few workflows for OpenMS 2.7

All new parameters were kept as default. New parameters were mostly found in FeatureLinkerUnlabe...

b5b323d2f398d30ad4da11fbf8c16b5e883088bb authored over 3 years ago by Eugen Netz <[email protected]>
Merge pull request #188 from OpenMS/feature/html

[Feature] html version with tex4ht

4bd1b838492a0fde85b3642f2e052c48b541a5b7 authored over 3 years ago by Julianus Pfeuffer <[email protected]>
Revert Css for inline pics

e6ccbd95959260cb7631374d4fd5f0447738eea0 authored over 3 years ago by Julianus Pfeuffer <[email protected]>
change

b288f3a20263a0ec8e5935699b2bfc6032278f2e authored over 3 years ago by Builder <[email protected]>
use a graphicsfolder

00f9466c47465db48c4429962b10a83be9355185 authored over 3 years ago by Builder <[email protected]>
copy images to separate folder

d7a4a0d36ff819c20769dec5b4de54fe07dc5abf authored over 3 years ago by Builder <[email protected]>
space?

af842c22cee27bef7b6d12a5fb819d37a4262ddd authored over 3 years ago by Builder <[email protected]>
fixed demacro

481f471a9154b49176994f4709b3a472e8ad4883 authored over 3 years ago by Builder <[email protected]>
parentheses?

5153b689b74f02b337da327870a3f720e1a8bf83 authored over 3 years ago by Builder <[email protected]>
forgot underscore escape

999647e24e620b53877e328292efc30be2692836 authored over 3 years ago by Builder <[email protected]>
reverted test stuff

f2b89ee5237e98c98a0db50467af3caed99e1988 authored over 3 years ago by Builder <[email protected]>
Use de-macro to avoid problems with macros in menukeys

0742f889c387edf428a25fe2fd85d7bedc061045 authored over 3 years ago by Builder <[email protected]>
added nice wrapper for menukeys package

92b1b754b3beabf463bfdaa0814166c5390ef827 authored over 3 years ago by Builder <[email protected]>
add bounding box files and many updates

db2ee05547aa1772528509abd51c103f51e964a7 authored over 3 years ago by Builder <[email protected]>
many fixes and styles

fb2638fbb0b677c0bc541dbf4d7be54414af4d21 authored over 3 years ago by Builder <[email protected]>
some styling changes

024691a0911b23f720c4053b48621be070f2acf4 authored over 3 years ago by Builder <[email protected]>
fix little error

0518f52d54a229afd6ddddaa933a9b545fb4963b authored over 3 years ago by Julianus Pfeuffer <[email protected]>
switch to minted package

6c559bbd6ffbe158adb872302f1e51cfc2dc79e5 authored over 3 years ago by Julianus Pfeuffer <[email protected]>
added some stuff for html generation

f4b47416705cb8262d789113b4bbc61595f1894e authored over 3 years ago by Builder <[email protected]>
Merge pull request #185 from OpenMS/release/2.6.0

[Update] PhosphoID

216093dc1aa68686bc7d643721c7dd512ddb06be authored about 4 years ago by Oliver Alka <[email protected]>
Merge pull request #184 from OpenMS/feature/phosphoID

Fixing bugs in Phosphoproteomics ID workflow

374974a9157df13dc09c03842342f9ed71085b57 authored about 4 years ago by Oliver Alka <[email protected]>
Delete redundant IDFilter node

1485c3996b3c5911107b19eb23a12adf2062bff1 authored about 4 years ago by JeeK <[email protected]>
Update version numbers

c7469bb64907e254932bdcd98b167134043b3c29 authored about 4 years ago by jpfeuffer <[email protected]>
Merge pull request #182 from OpenMS/release/2.6.0

Release/2.6.0

10db0b65eedf57ee0b9474db1b1135dd093fd454 authored about 4 years ago by jpfeuffer <[email protected]>
Updated QC workflows for OpenMS 2.6

f6fd32d0f0aa8fdd1bc77898b642482585079952 authored about 4 years ago by Eugen Netz <[email protected]>
add new MzTabReader node

55bbe8e87d16315f2e55b2b90773d521e39ea49c authored about 4 years ago by Timo Sachsenberg <[email protected]>
updated README

26d435c34359fe4d3cc5a3d8f95541333174f095 authored about 4 years ago by Timo Sachsenberg <[email protected]>
renamed Example_OneTool_ProteomicsLFQ_MSstats

deb239dea679b40330bd5f3e7491ce3b45c87ba0 authored about 4 years ago by Timo Sachsenberg <[email protected]>
Merge branch 'release/2.6.0' of https://github.com/OpenMS/Tutorials into release/2.6.0

1fa9b69c4f0206abb51813ffb17b94174a76d247 authored about 4 years ago by JeeK <[email protected]>
PhosphoproteomicsID changed: adding PeptideIndexer

069a8804d17abafb3d31a2593221d1b5d976a5d4 authored about 4 years ago by JeeK <[email protected]>
Merge pull request #180 from OpenMS/update/Handout_with_TRFP

Update handout with ThermoRawFileParser

7b4346fe34234762acb1c05b408482aab842dfc4 authored over 4 years ago by jpfeuffer <[email protected]>
Add files via upload

90c0bd665bf0cdbd09e35e07360ae60137ad6f25 authored over 4 years ago by Timo Sachsenberg <[email protected]>
Delete handout.xdv

b95933f714b0f037b31c8a7f85b82221a56adfc8 authored over 4 years ago by jpfeuffer <[email protected]>
Delete handout.pdf

f261df7c598ed392c77f1e4161908172db002206 authored over 4 years ago by jpfeuffer <[email protected]>
compile handout.tex

c452e7d097854874787803f05542a9b5c9a9bd92 authored over 4 years ago by Leon Bichmann <[email protected]>
add further entries to README - please append

1139d498ccc995ca490102a05caa9a6db181a522 authored over 4 years ago by oliveralka <[email protected]>
Merge branch 'release/2.6.0' of https://github.com/OpenMS/Tutorials into release/2.6.0

93c7beb7de05e40c6fe6e7da0cadf9c8400b9057 authored over 4 years ago by oliveralka <[email protected]>
rm Identification_quantification_isobaric_MSstatsTMT

9c557cdd9ab464e752205b263e1f5450c9292417 authored over 4 years ago by oliveralka <[email protected]>
Update README.MD

be1246dc5c13be1c6c4b0981f01aa2fa27481b16 authored over 4 years ago by Timo Sachsenberg <[email protected]>
Update README.MD

39a916db139f61fb9af43c9c73662d1b1af21be0 authored over 4 years ago by Timo Sachsenberg <[email protected]>
Update README.MD

2f84ec6460d0e4c4089e3f450f916f50ed53119b authored over 4 years ago by Timo Sachsenberg <[email protected]>
Create README.MD

eb49ff32a869d591abdcfdd97500404de2885735 authored over 4 years ago by Timo Sachsenberg <[email protected]>
updated to 2.6

cd2b62b79bca5186f017056ba0c9f4b7d581c995 authored over 4 years ago by Timo Sachsenberg <[email protected]>
Updated basic ID and Quant workflows to 2.6

623b393e6200531e8b92445cad41cee15bb674e9 authored over 4 years ago by Eugen Netz <[email protected]>
FIX MSstatsTMT

5fc1bdcb7017bf2fd5efe921da329e6bb2b522cf authored over 4 years ago by oliveralka <[email protected]>
add link example data - isobaric analysis

366b9c521105cc1ff6d18504292d399c0eab6278 authored over 4 years ago by oliveralka <[email protected]>
DIAMetAlyzer

f36467e943c59529847e164de2d9f05cc0938553 authored over 4 years ago by oliveralka <[email protected]>
move PH_ID; test MAG_WF

4b0e358eb2e90c5e3d70fa81e5cb0b7ffb0c812a authored over 4 years ago by oliveralka <[email protected]>
Metabolite_WF_2.6.0

0b6ba98b8b1f2e8d997416a5b78ac38821525e22 authored over 4 years ago by oliveralka <[email protected]>
Merge pull request #179 from OpenMS/feature/phospho_id

simple Phospho ID

8fa311ea368ada510d5ccb26596670eb363d7e55 authored over 4 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #178 from OpenMS/update/OpenSwathWorkflow_2.6.0

update OpenSwath.knwf for 2.6.0 release

c3f9a28967fd9dff5f97cb869fb1fdec639f17d8 authored over 4 years ago by Leon-Bichmann <[email protected]>
renamed vfile

0d847cfc83fd1aecec9849233076fc76241d04dc authored over 4 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #174 from OpenMS/feature/pLFQ_MSTATS

proteomics lfq workflow with MSStats

2702b9c0f258089ba2a4cc5ba9544041aa0f62d4 authored over 4 years ago by jpfeuffer <[email protected]>
Merge pull request #166 from OpenMS/oliveralka-patch-2

Workflow for isobaric analysis (untested)

c636f46c960db6890f474bc89d16498a2d162f31 authored over 4 years ago by jpfeuffer <[email protected]>
update OpenSwath knwf

81efb06fd5cede78315d20b4f7af453a456f62e0 authored over 4 years ago by Leon Bichmann <[email protected]>
Merge branch 'oliveralka-patch-2' of https://github.com/OpenMS/Tutorials into oliveralka-patch-2

c9fc587f181d9d79a4222b414c37b688d166a99b authored over 4 years ago by oliveralka <[email protected]>
add MSstatsTMT and results

7faec92b91e4923f96cce49dd7e453a8cd933712 authored over 4 years ago by oliveralka <[email protected]>
Merge branch 'master' into oliveralka-patch-2

ef3f2db5b0a29a532e68516a9d163b49f63be80b authored over 4 years ago by Oliver Alka <[email protected]>
rewrite - unfinished

c94c436b62ac2d1f9556eac11494a948e55ec248 authored over 4 years ago by oliveralka <[email protected]>
Merge pull request #176 from oliveralka/add/DIAMetAlyzer_tutorial

[DRAFT] OpenSWATH for Metabolomics

267c3148d4d03559cece725fdf651e4094609211 authored over 4 years ago by jpfeuffer <[email protected]>
ADD: req. changes

39d2cb1275791145a3ccc185270fe9d8a385d3bd authored over 4 years ago by oliveralka <[email protected]>
switch to paragraphs

9c001fbefa23376236db09331931ab514279dfb6 authored over 4 years ago by oliveralka <[email protected]>
ADD: Paragraph & WF configuration

a33ea4a915fa32a97057252884c8e6826684c702 authored over 4 years ago by oliveralka <[email protected]>
Update Tutorial

0d0f1aa2d27648ac8ae0be0ba32637cae5f3d902 authored over 4 years ago by oliveralka <[email protected]>
Add MSstatsTMT R script to workflow.

feea4b95efa3d873e337806232e0fed7b9d9631c authored over 4 years ago by Julianus Pfeuffer <[email protected]>
Check parameters of the workflow

1af9605ab5fc3c48d89876e411f82118ffe8242d authored over 4 years ago by oliveralka <[email protected]>
Describe special values.

10efe46f17b4f73a97308b51d942e41b07dc8ddc authored over 4 years ago by jpfeuffer <[email protected]>
Update isobaric.tex

c1a6cee5fe71f7629a0035a2e96fea8230d67427 authored over 4 years ago by jpfeuffer <[email protected]>
FIX: figure

ef53647788d9171f0af5d189c9c483e5494c5588 authored over 4 years ago by oliveralka <[email protected]>
[DRAFT] OpenSWATH for Metabolomics

8fc48f535910763dadfb6c6a0a15680b91aa96a1 authored over 4 years ago by oliveralka <[email protected]>
Draft version of an ID only Phosphoproteomics workflow

67a482a58ab692b982833ed68be65232667e97eb authored over 4 years ago by Timo Sachsenberg <[email protected]>
proteomics lfq workflow with MSStats

e92ff0dccc8bd4b7666785ddce9e9c671c92dfe4 authored almost 5 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #172 from OpenMS/updateVer25

update Versions

ef199be8e82364d104d143600b069a45cc9cee18 authored almost 5 years ago by Timo Sachsenberg <[email protected]>
Merge branch 'oliveralka-patch-2' of https://github.com/OpenMS/Tutorials into oliveralka-patch-2

9f91839342a0054c6a59443f2e296245a9faada0 authored almost 5 years ago by oliveralka <[email protected]>
[RM] inference, [ADD] Edited WF, Draft explanation experimental design

2e7ef24e53408418e5c3ea57dfa3747a486769a4 authored almost 5 years ago by oliveralka <[email protected]>
Update isobaric.tex

e760ec085d0284248ede9f2c8127367c1deeb4dc authored almost 5 years ago by jpfeuffer <[email protected]>
update Versions

d9b68d16d00f0e882c8246d5a917e546ef558477 authored almost 5 years ago by jpfeuffer <[email protected]>
[ADD] Draft for Tutorials, [UPDATE] workflow use epifany for inference

4be53fb632a805a00a765509f43d8560876820bd authored almost 5 years ago by oliveralka <[email protected]>
Merge pull request #170 from oliveralka/bugfix/master

[FIX] general

6a2c7c143115f8b2a54bcda6a76be4f9c50b8ac5 authored almost 5 years ago by Timo Sachsenberg <[email protected]>