Code

Development#6

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Maiykol merged 60 commits intoproductiondrugst-one/backend:productionfrom developmentdrugst-one/backend:developmentCopy head branch name to clipboardOct 9, 2024

+20-2

Commits

Commits on Mar 15, 2024

• first draft of pathway enrichment

  lspindler2509

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  a19b87b

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Commits on Mar 16, 2024

• adjusted string according to frontend

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  38b3bc9

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Commits on Mar 18, 2024

• parse own gene sets accordning to parameters (needed for background), filter by adjusted p-value

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Commits on Mar 19, 2024

• deleted unnecessary parameters, added background

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• always use symbol graph since genesets are based on symbol idspace

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• start to parsing result, no empty string anymore in genes of geneset, mapping of pathway

  lspindler2509

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Commits on Mar 20, 2024

• create networks

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Commits on Mar 24, 2024

• draft on rsult output

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Commits on Mar 25, 2024

• added progress steps for frontend, added groups to config

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Commits on Mar 26, 2024

• adjust config name

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• deleted unnecessary print

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Commits on Mar 28, 2024

• deleted unnecessary import/logs, added drugstonetype

  lspindler2509

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  9c85723

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• added genesets in all idspaces, added odd_ratio, could delete mapping of idspaces

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Commits on Mar 31, 2024

• only parse one pathway and when switching geneset/pathway, calculate chosen one

  lspindler2509

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• only add groups for pathway enrichment, if not availale in config

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Commits on Apr 1, 2024

• added create_geneset api that can be called from postman etc.

  lspindler2509

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Commits on Apr 3, 2024

• added isSeed, adjustments in logging

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  6c21029

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• added documentation to pathway enrichment

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• different colour for overlap since previous colour already used for foundNode

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Commits on Apr 7, 2024

• add edges api

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Commits on Apr 8, 2024

• added louvain clustering (edges not filled from ppi graph yet)

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Commits on Apr 9, 2024

• use distinctipy for colour coding

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  54941b7

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• deleted unnecessary import

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  18e6e64

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• add edges from interaction graph, possibility to ignore isolated nodes in clustering

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Commits on Apr 10, 2024

• delete logs, round percentage

  lspindler2509

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  f6e8bbd

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• new group for added nodes

  lspindler2509

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Commits on Apr 15, 2024

• only use chosen nodes and not whole input network

  lspindler2509

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  f2b960a

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Commits on Apr 17, 2024

• round odds ratio

  lspindler2509

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Commits on Apr 22, 2024

• preperations for download of pathway enrichment, clustered proteins

  lspindler2509

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Commits on Apr 23, 2024

• add cellular component to DB

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Commits on Apr 24, 2024

• add cellular component for all idspaces but ensembl

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  b0cfece

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• some fixes for cellular components

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Commits on Apr 25, 2024

• add cellular component for ensembl

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Commits on Apr 29, 2024

• add layer determination

  lspindler2509

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• map layer in backend

  lspindler2509

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• add layouting

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Commits on Apr 30, 2024

• fixed order for layers

  lspindler2509

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• add random layout

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  f06fbad

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Commits on May 3, 2024

• start pathway enrichment with tableview

  lspindler2509

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  cf9c607

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• added leiden clustering

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• added references

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Commits on May 5, 2024

• parse file in backend

  lspindler2509

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• use default node group

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Commits on May 9, 2024

• add default node group

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• parse .gt files

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Commits on May 10, 2024

• updated/added documentation to backend task

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• delete old code

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Commits on May 13, 2024

• optional group attribute for .gt and .graphml

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Commits on May 16, 2024

• check if nodes in graph

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Commits on May 24, 2024

• added gseapy version

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• added versions

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Commits on Jul 23, 2024

• Merge branch 'production' into development

  Maiykol

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Commits on Aug 26, 2024

• Merge remote-tracking branch 'upstream/development' into pathway-enrichment

  lspindler2509

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• delete old test file

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  b6b8ec7

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Commits on Sep 10, 2024

• adjusted import

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Commits on Sep 17, 2024

• Merge pull request #5 from lspindler2509/pathway-enrichment

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  AndiMajore

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Commits on Oct 8, 2024

• Merge branch 'development' of github.com:drugst-one/backend into development

  Maiykol

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• revert pathway merge

  Maiykol

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Commits on Oct 9, 2024

• bugfix for custom_edges input bug

  Maiykol

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• Merge branch 'production' into development

  Maiykol

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