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v0.29.0 - cbio, opentargets, bgee and more

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@lauraluebbert lauraluebbert released this 26 Sep 02:07
· 95 commits to main since this release
5589dee
  • New modules:
  • gget enrichr now also supports species other than human and mouse (fly, yeast, worm, and fish) via modEnrichR
  • gget mutate:
    gget mutate will now merge identical sequences in the final file by default. Mutation creation was vectorized to decrease runtime. Improved flanking sequence check for non-substitution mutations to make sure no wildtype kmer is retained in the mutation-containing sequence. Addition of several new arguments to customize sequence generation and output.
  • gget cosmic:
    Added support for targeted as well as gene screens. The CSV file created for gget mutate now also contains protein mutation info.
  • gget ref:
    Added out file option.
  • gget info and gget seq:
    Switched to Ensembl POST API to increase speed (nothing changes in front end).
  • Other "behind the scenes" changes:

fixes #157
fixes #121
fixes #144
fixes #140
fixes #103