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ampvis2 tutorial first upload#4968

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lenaarenot wants to merge 83 commits intogalaxyproject:maingalaxyproject/training-material:mainfrom lenaarenot:ampvis2_tutorialfirst_uploadlenaarenot/training-material:ampvis2_tutorialfirst_uploadCopy head branch name to clipboard

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Commits on May 14, 2024

• Create new tutorial.md

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• Merge pull request #1 from lenaarenot/lenaarenot-ampvis2_heatmap

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Commits on May 22, 2024

• Merge branch 'galaxyproject:main' into main

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Commits on May 24, 2024

• Merge branch 'galaxyproject:main' into main

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• added the first section of tutorial.md

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Commits on Jun 4, 2024

• move toturial, remove wrong md

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• Update topics/microbiome/tutorials/visualisation-ampvis/tutorial.md

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• Merge branch 'galaxyproject:main' into ampvis2_tutorialfirst_upload

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• Merge branch 'galaxyproject:main' into main

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• Merge branch 'galaxyproject:main' into ampvis2_tutorialfirst_upload

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Commits on Jun 15, 2024

• updated text in tutorial.md, tutorial.bib, added images folder

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Commits on Jun 19, 2024

• add lena as contributor

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• merge with remote

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• revert

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• change version

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• fixed images and citations

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• fixed citations

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Commits on Jun 20, 2024

• updated text and added more citations

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• tried note boxes insted of note in a text

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Commits on Jun 24, 2024

• added question boxes and updated text

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Commits on Jun 26, 2024

• updated rarefaction section

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• fixed first wuestion box

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• fixed first question box again

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• added hands-on how to preparedatasets out of 1 excel sheet

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• fixed first question box again

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• fixed first questions box image

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• fixed first questions box image 2.0

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• fixed first questions box image 3.0

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• fixed first questions box image 4.0

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• added last missind question section

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• removed to_do

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Commits on Jun 27, 2024

• checked language for consistend formulation, added conclusions, added data upload tutorial reference

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Commits on Jun 28, 2024

• reformulated rarefaction curve theory

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• eddited paragraph, deleted 'note:' from comments

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Commits on Jun 29, 2024

• apdated zenodo names, plus zenodo link

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• apdated zenodo names, plus zenodo links (manualy)

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• a try to add tools and workflows

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• fixed links

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Commits on Jul 2, 2024

• added section 'uploading biom and creating phyloseq files'

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Commits on Jul 3, 2024

• restructured introduction section

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• forgot a '.'

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Commits on Jul 4, 2024

• added zenodo links and snipets to rarefaction, heatmap and boxplot

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• edited zenodo links and added snipets to ordination

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• tried eliminating tool links

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• yaml file problems

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• yaml file problems

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• yaml file problems

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• tried eliminating tool links

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• cosmetic make over

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• rarefaction section with sort/long versions

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Commits on Jul 5, 2024

• rest of sections with short/long versions

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• restructure and trying to fix linkage to 'datasets'

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• restructure and trying to fix linkage to 'datasets'

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Commits on Aug 24, 2024

• updated text on amplicon backgroud, visualisation tools, ASV vs OTU, use case numbering, heatmap tip, new heatmap figures, subsampling and grouping

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• use case numbering fix

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• use case numbering fix

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Commits on Sep 5, 2024

• updated text on heatmap, all ordination section, boxplot

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• fixing links

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• fixing links

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Commits on Sep 13, 2024

• better heatmap pictures

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Commits on Sep 19, 2024

• restructured use case 2 and 3 with separated tool and workflow

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• fixing small errors

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Commits on Sep 25, 2024

• separated rerafaction section in tools, changed ampvis load and subsamples to tools

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Commits on Oct 18, 2024

• manually took over all correction suggestions and made bullet points start with capital letter

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• fixing not rendered comment

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• fixing not rendered comment

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• adding lotus2 and merginh mothur tools to 1 bullet point

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• correct comment style

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• bullet points of formats

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• specific zenodo link representation

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• specific zenodo link representation for use case 1

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• specific zenodo link representation for use case 1 v2

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• specific zenodo link representation for use case 1 v3

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• specific zenodo link representation for use case 1 v4

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• made biom and phylosec a subsection

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• rephrasing the part of Kraken and MataPhlAn

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• testing link optics

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• bullet points of ploting types with link

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• bullet points of ploting types with link + fixing paragraph look

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• rephrased all 'we' sentances to passive voice

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Commits on Oct 25, 2024

• specific zenodo link representation for use case 1 and 2 v5

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• plot types final links

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Commits on Dec 5, 2024

• Merge branch 'main' into ampvis2_tutorialfirst_upload

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