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

small additions to MSStats R workflow description.

60f78a34dcfcc0572be58676cdf46b83b669e6ee authored over 6 years ago by Julianus Pfeuffer <[email protected]>

Updated file links on USB stick and update site

8711d2b54bb85c088f7672b18e82a3d4a2c0f747 authored over 6 years ago by Julianus Pfeuffer <[email protected]>

MSstats installation (#123)

* MSstats installation

* Updated R installation

4a0e79fd5add1e92c0d233e6712136ba5eb4f2da authored over 6 years ago by Marc Rurik <[email protected]>

Minor fixes.

01c63e970a898e4fe3c4c25b9203d016c05daf48 authored over 6 years ago by Julianus Pfeuffer <[email protected]>

Added the MSstats workflow with all the R nodes that produces e.g. the c2-c1 plot.

d7a7d606109f6217f5628473812073ba1d4270bb authored over 6 years ago by Julianus Pfeuffer <[email protected]>

Remove pdf from .gitignore

7ecb902625600a4b34f9ddd36a6beafb07bc0c4e authored over 6 years ago by lukaszimmermann <[email protected]>

PCA replace ggbiplot to ggfortify -> update import (#125)

The most current(?) PCA Snippet switched to ggfortify instead of ggbiplot (which required devtoo...

c091b91f037681915d648c0fb2d0ef7f227d1dd4 authored over 6 years ago by FabianAicheler <[email protected]>

[ADD] Description of group comparison matrix

a9ab30fe28a8b511dc79020e10f43ddade88ed33 authored over 6 years ago by lukaszimmermann <[email protected]>

[ADD] MSstats R workflow nodes figure

ebc00ac88c7d719442ddbf31c3534de406d92d91 authored over 6 years ago by lukaszimmermann <[email protected]>

[UPDATE] Update Workflows 2018

21a73b598c2d0d96c23c928a0bbb0411bba39496 authored over 6 years ago by Oliver Alka <[email protected]>

Some more changes

d781f1e1f6d6708705d71e10db3a0d2fc4f1363c authored over 6 years ago by Julianus Pfeuffer <[email protected]>

[ADD] Some text and plots for MSstats analysis in R. To be continues

0cc3f80ebcd3443ee3c48584d6e566cd26de5515 authored over 6 years ago by lukaszimmermann <[email protected]>

Further additions. Beginning of the MSstats analysis workflow

abd891f0138b0c25d15d356b6f10d971b6afeebc authored over 6 years ago by Julianus Pfeuffer <[email protected]>

Fixes and smaller additions.

dae1d377093e1b9300365bc5f6e4051dad2299c1 authored over 6 years ago by Julianus Pfeuffer <[email protected]>

Fixes and TODOs

fbf94122f1b5d6297953e13701f5c3a16b84c643 authored over 6 years ago by jpfeuffer <[email protected]>

[DOC] introduce tabularx; style;

efaf26750c0ae8acd82bc41b1c5eb2f2cf79e63c authored over 6 years ago by Oliver Alka <[email protected]>

[FIG] add identifcation and quantifiaction workflow wo MSstatsConverter

6a3de188765c42c5c7ac7307eb79550ca4eaa6e8 authored over 6 years ago by Oliver Alka <[email protected]>

[DOC] Changed layout; fix tables; explanation of workflow

3ce804c9aee56e72a40e7814a924a4e7fe95c0c8 authored over 6 years ago by Oliver Alka <[email protected]>

[DOC] add table layout (Samples); citation MSstats; Style introduction

ae5dc2f12812f74fd9dc80ff9cb069ef1dc4cb91 authored over 6 years ago by Oliver Alka <[email protected]>

[DOC] add citation; add experimental design & dataset table

62fe75212f27f7ae13cfbee39b29819229dc7f5f authored over 6 years ago by Oliver Alka <[email protected]>

[DOC] Draft for MSstats iPRG tutorial

60f0a9dc07f949378155177c9c5e2c87ac7c119a authored over 6 years ago by Oliver Alka <[email protected]>

only label-free part

5d0840880888aaca60eb2cfd5d7e4b37cf7d0ff2 authored over 6 years ago by timosachsenberg <[email protected]>

Add files via upload

c9183f98b162833cbca59e6d71a5ae3cc4375b31 authored almost 7 years ago by Timo Sachsenberg <[email protected]>

Add files via upload

55600efb5289440e7891d289ebe881b327533d8d authored almost 7 years ago by Timo Sachsenberg <[email protected]>

[FIX] Issues (#122)

* [ADD] Update links install software KNIME

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

7c9d78a577fade434d819535e38afa70a7b50aaa authored about 7 years ago by oliveralka <[email protected]>

[FIX] req. changes

c67ac3f592f4a342a661e2eeabb0c89d995fd139 authored about 7 years ago by Oliver Alka <[email protected]>

[FIX] mark digression, hihglight advanced param, explain light gray advanced params

ed918f5ae021971101dabdb5f029e81073de3861 authored about 7 years ago by Oliver Alka <[email protected]>

[ADD] changes of changes

957da7750712988ba36d441319a4afec7a875a1f authored about 7 years ago by Oliver Alka <[email protected]>

Merge remote-tracking branch 'upstream/master'

994cde62c04c66c71b28bd9183ccbe1eec7b9ff4 authored about 7 years ago by Oliver Alka <[email protected]>

[ADD] column header

[ADD] explain manual validation
[ADD] remove copy spectral lib

06433ad8bbad3342fd97ecb5d63a7a2110032b39 authored about 7 years ago by Oliver Alka <[email protected]>

[ADD] Update links install software KNIME

f397ed5d8d5ddb4b2721496e48033e35173e7f5f authored about 7 years ago by Oliver Alka <[email protected]>

[ADD] Update links install software KNIME

8f1eb68b76884583cde2717a3dff3f88198de538 authored about 7 years ago by Oliver Alka <[email protected]>

[Fix] Fixed no line to end error and some warnings.

1760c965511e3a44989e841efac8a877ef6cbb31 authored about 7 years ago by Julianus Pfeuffer <[email protected]>

removed reference to FUll installer

ac683b7aa1fc3644eb012fcb1d3023a04ffa99eb authored about 7 years ago by Timo Sachsenberg <[email protected]>

[TUTORIAL] manual merge of new stuff in EBI2017

7d78d16a5ba3c9cb1407d567b60da21f94d9c088 authored about 7 years ago by timosachsenberg <[email protected]>

Update README.md

db83846972b1fee52bf4367c8a4a0c535d54abdd authored about 7 years ago by jpfeuffer <[email protected]>

Update README.md

05017b592ea88912c9770a632b4ca18493817395 authored about 7 years ago by jpfeuffer <[email protected]>

Update README.md

fa92c2c4705f856fc1c36cbe8168c0d8347a370b authored about 7 years ago by jpfeuffer <[email protected]>

Update README.md

835fad4c4110d71291689c657614ab147fcc882e authored about 7 years ago by jpfeuffer <[email protected]>

[EDIT] R Code Meta, Explanation SpectralID

5f9b5068d7bbd14bf5b357dd5dffea28a7c0c09e authored over 7 years ago by Oliver Alka <[email protected]>

Merge pull request #77 from OpenMS/mwalzer-tutorial2017-patch-lnx

corrected path for Complete consensus identification workflow figure

70bc789751a1b0d3298fb418aa884c0e8c817142 authored over 7 years ago by Hannes Roest <[email protected]>

corrected path for Complete consensus identification workflow figure

97f621c5496bb0031a1bc20edbfa53fad47b3661 authored over 7 years ago by Mathias Walzer <[email protected]>

Added higher resolution logo with transparent bg.

5fe108238f3997e4bdb55b6448d66ec57b716806 authored over 7 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #75 from jpfeuffer/master

Merges Boston2017 in and adds Elixir logo

17f2eab7a226ffddfb2ee78209c9f18163848cca authored over 7 years ago by jpfeuffer <[email protected]>

Added Elixir logo and revamped title page

4c38af08ade420081b90bddd5f5efc7a4b3ac430 authored over 7 years ago by Julianus Pfeuffer <[email protected]>

Reenabled all chapters.

b7127e4f7a852b2792119d6826a1792efdf80117 authored over 7 years ago by Julianus Pfeuffer <[email protected]>

Medium changes and fixes. Figure reference, unified style of keys, menu items...

1e7292cc012c0efb318fae9956bef1fd768f0711 authored over 7 years ago by Julianus Pfeuffer <[email protected]>

fix mac plugin folder

e5a522c6f08b6cfcf003dade1fdc4a1a2728daac authored over 7 years ago by Timo Sachsenberg <[email protected]>

fixed plugin identifier

f6cdb821a1c089310d2a161d7b69e580a2fdc9e5 authored over 7 years ago by Timo Sachsenberg <[email protected]>

Merge branch 'feature/BOSTON2017' of https://github.com/OpenMS/UMTutorials into feature/BOSTON2017

f2014a6b6582ddaa178654fa506ccdc6727c5863 authored over 7 years ago by Timo Sachsenberg <[email protected]>

added URL to link

4564c876aab44390bd56c5483808a57b10b50050 authored over 7 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #69 from jpfeuffer/feature/BOSTON2017

Changed path representation. Added path for Mac in MTX part.

524926502c722a5d5cd3cd88c77596acad2f5e76 authored over 7 years ago by Timo Sachsenberg <[email protected]>

Merge branch 'feature/BOSTON2017' into feature/BOSTON2017

9ac3bdca9b2d1a09796d90b212367e7a59440f03 authored over 7 years ago by jpfeuffer <[email protected]>

Changed path representation. Added path for Mac in MTX part.

cde5b9fdb43d036d77ca1ebcb8765d2eac6d9e75 authored over 7 years ago by Julianus Pfeuffer <[email protected]>

changed backslashes back to arrows

6e7b076e819c866d897fafa3a8207d0c9bc8bd22 authored over 7 years ago by Timo Sachsenberg <[email protected]>

updated some images to new KNIME style

39528facd2850fb4627d20d50d66a03e2a7f79d7 authored over 7 years ago by Timo Sachsenberg <[email protected]>

added workflow

78d4b819829bb2274c6ec8624060cebac4d0cd2e authored over 7 years ago by Timo Sachsenberg <[email protected]>

added metabolite id with spectral libraries

17480425acccac9fcd19d029b530af96f8277d67 authored over 7 years ago by Timo Sachsenberg <[email protected]>

added raw example file path

8fe9ec91003a6f463347dfb0771e7dd1e45e1d43 authored over 7 years ago by Timo Sachsenberg <[email protected]>

ProteoWizard section extended

6dab1df9e72100d2d201901c190477eb1b6ae114 authored over 7 years ago by Timo Sachsenberg <[email protected]>

fixes shift key misconception https://github.com/OpenMS/Tutorials/issues/61

9a38dd6092754ca69831c49edfcbd8abd323be42 authored over 7 years ago by Timo Sachsenberg <[email protected]>

fixes https://github.com/OpenMS/Tutorials/issues/63

313b70751770a711f59b4d1720556ff887d4d1e8 authored over 7 years ago by Timo Sachsenberg <[email protected]>

disabled unused chapters

14afbe71ca1ac67fdfe969d46e051a0384d229b8 authored over 7 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #67 from OpenMS/jpfeuffer-patch-1

Added FAQ about a weird behaviour.

eb0b15c52fc38e7768fbe0af89bc0db1acdd7af4 authored over 7 years ago by jpfeuffer <[email protected]>

Added FAQ about a weird behaviour.

9929e1161b97c1038ffd4a09c6e84759cc83033c authored over 7 years ago by jpfeuffer <[email protected]>

Merge pull request #64 from cbielow/master

[FIX] compile handout (MikTex)

acc63d61d33f94a65b894d924f08f42ef922c86d authored almost 8 years ago by jpfeuffer <[email protected]>

[DOC] modified comments

1970c4df37ad29e24839f3edb97adb2eb8cd9ac4 authored almost 8 years ago by Chris Bielow <[email protected]>

[FIX] rename font names (a space in `Ubuntu Mono` prevents Tex on Windows from finding it). Also, use ./fonts/ as Path hint (since font is not installed by default)

3293b8c05fc3f23b1ed13433663b410f90653814 authored almost 8 years ago by Chris Bielow <[email protected]>

[DOC] extended README a bit

7680ffa8016f283e9253ae1ea841bced6a97f740 authored almost 8 years ago by Chris Bielow <[email protected]>

Added remark about numerical precision in KNIME tables to FAQ

52690a10697ca500aadd1e6071d614a325d9314e authored almost 8 years ago by jpfeuffer <[email protected]>

Update of filenames and FAQ

2bfc88e30c8eb82ed9b0a484c17e156d547d9a6f authored almost 8 years ago by Julianus Pfeuffer <[email protected]>

Untoggled prerelease

49197c89b55590c2f8f3156563c4e1cdd4cab644 authored almost 8 years ago by Julianus Pfeuffer <[email protected]>

Update KNIME update site version.

72ec3b12191c962c044c46109dc577c186cc4d5e authored almost 8 years ago by Julianus Pfeuffer <[email protected]>

Update KNIME version and made full installer the standard.

30f7a1f8a5676618eb723ca9dda8353385ba2ef4 authored almost 8 years ago by Julianus Pfeuffer <[email protected]>

R node problems on macOS FAQ

001e351e6cfb3ceeaf68d906f8bbad739d39b3a0 authored about 8 years ago by jpfeuffer <[email protected]>

Addressed errors from UM2016

ef5579dd2a058e02127de042d5f3a27b9ef6d440 authored over 8 years ago by Julianus Pfeuffer <[email protected]>

no message

418be11e04ec299d256bb38c44d2ffdc9fcf49f6 authored over 8 years ago by Timo Sachsenberg <[email protected]>

Changes

52aa8a03e12b07f7a093f8aaae8a7742b3e6dd95 authored over 8 years ago by Julianus Pfeuffer <[email protected]>

Changed installation instructions for pyopenms.

9a6d1c060ed87cf99306ddc23a6f1af96003948a authored over 8 years ago by Julianus Pfeuffer <[email protected]>

More changes.

1b967765b3a342e7b7fa52a1579b83df91179aac authored over 8 years ago by Julianus Pfeuffer <[email protected]>

Added updated figure.

498ebb57c5fcf588842483aa27699f4ae23ea7ca authored over 8 years ago by Julianus Pfeuffer <[email protected]>

Large changes to tutorial. Especially to adapt to some changes in the inference workflow.

d296ff676f1ce714700815d7a988b61f3cbed018 authored over 8 years ago by Julianus Pfeuffer <[email protected]>

Updated protein inference WF. Renamed, since it is coupled with quant. Updated settings. Exchanged OMSSA with XTandem. Added MzTabExporter.

2f4e057836496da0601aca3fe991542d149a901d authored over 8 years ago by Julianus Pfeuffer <[email protected]>

OpenSWATH

cff6112e10300f549949752a7d46ba2fab3ee9e6 authored over 8 years ago by Timo Sachsenberg <[email protected]>

added QC metanodes

bfe92215060b5ec1ec605231e5226865376b5e02 authored over 8 years ago by Timo Sachsenberg <[email protected]>

copied workflows from GCB2016 branch and consensus workflow

739db160b2e3206add1447cec75222457729c6f4 authored over 8 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #50 from jpfeuffer/feature/updateFAQ

Feature/update faq

d9f9f19b2eaaa80f5d0c10d85d3c3645af54e812 authored over 8 years ago by Timo Sachsenberg <[email protected]>

Added more explanation for a red light.

193f635e6ddf8cebd87b06d2009301720420a179 authored over 8 years ago by Julianus Pfeuffer <[email protected]>

Reformatting.

49d0e3877181d64acda9cb8fc09cf8421ba5bb1b authored over 8 years ago by Julianus Pfeuffer <[email protected]>

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

22b4821e28c1497d0637da9b3ad322ded78231c2 authored over 8 years ago by Julianus Pfeuffer <[email protected]>

Expanded troubleshoot.

2d1856252e7c9c7e9dae5006f5bcc175a846c03e authored over 8 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #46 from mwalzer/feature/update_readme

[NOP] update readme

ee1f334a3037328ff03614fc816bc2e026222ec9 authored over 8 years ago by Mathias Walzer <[email protected]>

[NOP] amend to readme

076f6f82d3ff19a99e601a52b7f9c1e6fbcdd6c2 authored over 8 years ago by mwalzer <[email protected]>

[NOP] update readme

fbcd5bcbae23401f385c920229343675470ed748 authored over 8 years ago by mwalzer <[email protected]>

Merge pull request #45 from mwalzer/feature/updating.gitignore

[NOP] removed mac pollution and added to .gitignore
will go ahead with the merge due to the min...

068b0d7daf09cddae0c5488b967818e371b9b40f authored over 8 years ago by Mathias Walzer <[email protected]>

[NOP] removed mac pollution and added to .gitignore

80597937fbecd69aa790c6dfd63b206f10629f18 authored over 8 years ago by mwalzer <[email protected]>

Merge pull request #40 from FabianAicheler/patch-4

labelfree, minor changes

6fd4a27956ac93231c9092f54d36f1fec050b740 authored over 8 years ago by Mathias Walzer <[email protected]>

Merge pull request #41 from FabianAicheler/patch-6

fixed link to pyOpenMS docu

369be919400c01f80550a108c5fe53c0c15f2d81 authored over 8 years ago by Mathias Walzer <[email protected]>

Merge pull request #42 from FabianAicheler/patch-5

OpenSWATH section, fixed figure reference, .zip Path

100c44c6f107389843f4ab256c167d2a67edcb95 authored over 8 years ago by Mathias Walzer <[email protected]>

Merge pull request #44 from FabianAicheler/patch-8

Metabolomics: Mostly added/updated node paths, typos

3defd7783767525766c323fa7ff870a507ee78fa authored over 8 years ago by Mathias Walzer <[email protected]>