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Enable synonym mapping without "gprofiler" #14

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bschilder opened this issue Feb 20, 2022 · 0 comments
Open

Enable synonym mapping without "gprofiler" #14

bschilder opened this issue Feb 20, 2022 · 0 comments
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enhancement New feature or request

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@bschilder
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Functions like map_genes and aggregate_genes rely on "gprofiler" as the only method that can do gene synonym matching.

However, this requires internet access and the gprofiler databases sometime breaks down randomly.
For example, today during checks:

── Error (test-run_benchmark.R:3:5): run_benchmark works ───────────────────────
Error in `gprofiler2::gconvert(query = ranges, organism = species, ...)`: Bad request, response code 400
Backtrace:

Would be good to have non-gprofiler alternatives for all functions, including these.

@bschilder bschilder added the enhancement New feature or request label Feb 20, 2022
@bschilder bschilder added this to the Publish orthogene preprint milestone Oct 23, 2023
@bschilder bschilder self-assigned this Oct 23, 2023
@bschilder bschilder modified the milestones: Publish orthogene preprint, Publish orthogene manuscript Oct 23, 2023
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