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Add bridge ortholog mapping - #504

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ivokwee wants to merge 17 commits into
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bridge-ortholog
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Add bridge ortholog mapping#504
ivokwee wants to merge 17 commits into
edgyfrom
bridge-ortholog

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@ivokwee

@ivokwee ivokwee commented Jul 24, 2026

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Add bridge orthology search for poorly annotated species. Bridge orthology search uses an intermediate species (BRIDGE_SPECIES = dmelanogaster, drerio, celegans, scerevisiae, athalian) to map an organism first, then using the bridge species maps to human orthology next. This can improve orthology mapping for poorly annotated species (like Fall armyworm). Better orthology mapping is useful for geneset analysis, drug connectivity and experiment similarity in OPG.

@ivokwee
ivokwee requested a review from ESCRI11 July 24, 2026 07:42
@ESCRI11

ESCRI11 commented Jul 27, 2026

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current state of PR does not even parse

Error in FUN(X[[i]], ...) : 
  /playbase/R/pgx-annot.R:1443:1: unexpected '}'
1442:   return(top_match)
1443: }
      ^

please fix before i can try to run it and review

@ivokwee

ivokwee commented Aug 1, 2026

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@ESCRI11 ok. try again.

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3 participants