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improve-species#499

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ivokwee wants to merge 13 commits into
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improve-species
Open

improve-species#499
ivokwee wants to merge 13 commits into
edgyfrom
improve-species

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@ivokwee

@ivokwee ivokwee commented Jul 14, 2026

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Species table improvements and annotation cleanup.

  • Improved from 301 to 1581 organisms. We take union of supported organism from AnnotHub and Gprofiler (previously we took intersection)
image - Updated SPECIES_TABLE - Minimize use of orthogene. Internal database seems old and did not recognize armyworm. - Got list of gprofiler list directly using API instead. - Several change of non-exported functions in pgx-annot.R to show internal use

NB: 90% manually implemented & tested

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ivokwee requested a review from phisanti July 14, 2026 21:54
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ivokwee marked this pull request as draft July 15, 2026 07:17
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ivokwee commented Jul 15, 2026

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testing with dataset now.

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ivokwee marked this pull request as ready for review July 15, 2026 14:36
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ivokwee marked this pull request as draft July 15, 2026 17:00
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ivokwee marked this pull request as ready for review July 16, 2026 11:32
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ivokwee commented Jul 16, 2026

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tested with armyworm. ok.

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