Issues

• Over-prediction of gene models during online annotation of plant genomes

  usadellab/Helixer#223 · Filter by author liqianghou2022 opened on Aug 15, 2026
  2

• During the teast run, Helixer did not use GPU

  usadellab/Helixer#218 · Filter by author jyw-atgithub opened on Jun 14, 2026
  7

• [Questions] How does Helixer handle Transposable Elements?

  usadellab/Helixer#216 · Filter by author crakshay1 opened on May 8, 2026
  4

• [Feature Request] - Protist model

  usadellab/Helixer#214 · Filter by author jolespin opened on Apr 2, 2026
  3

• Short exons account for a large proportion

  usadellab/Helixer#193 · Filter by author linyuiz opened on Nov 7, 2025
  2

• Add UTR region on exsisting gff files

  enhancement
  usadellab/Helixer#181 · Filter by author bioyoshoo opened on Jun 13, 2025
  1

• Coordinates Differences in Predicted Models Between GPU and CPU Runs

  usadellab/Helixer#172 · Filter by author apollo994 opened on Feb 25, 2025
  4

• over-prediction small contigs

  enhancementevaluationperformance
  usadellab/Helixer#147 · Filter by author mhooykaas opened on Oct 30, 2024
  4

• Micro exons with single bases or two

  enhancementevaluationperformance
  usadellab/Helixer#138 · Filter by author ke-shi opened on Jul 31, 2024
  8

• sqlite3.DataError: string or blob too big

  data format
  usadellab/Helixer#132 · Filter by author arslan9732 opened on Jun 9, 2024
  2

  

• gff3 specification

  data format
  usadellab/Helixer#127 · Filter by author nhartwic opened on May 10, 2024 · v0.3.5
  1

• Low busco scores for transcripts called on large Cupressus genome (10Gb) with helixer

  enhancement
  usadellab/Helixer#126 · Filter by author Bios4Biol opened on Apr 19, 2024
  2

• Some tensorflow warning/error messages when running Helixer via Singularity

  usadellab/Helixer#123 · Filter by author spoonbender76 opened on Apr 11, 2024
  4

• Add Helixer to conda

  enhancement
  usadellab/Helixer#104 · Filter by author xiekunwhy opened on Jul 19, 2023
  4

• [Question] Can this be used broadly for all microeukaryotes (e.g., fungi, protists, etc)?

  usadellab/Helixer#100 · Filter by author jolespin opened on Jun 3, 2023
  8

• change transition matrix to only include correct transitions from geenuff

  usadellab/Helixer#90 · Filter by author alisandra opened on Feb 2, 2023

• record seed / random state

  enhancement
  usadellab/Helixer#89 · Filter by author alisandra opened on Jan 24, 2023
  

• Evaluate new training datasets

  enhancement
  usadellab/Helixer#63 · Filter by author soi opened on Jul 22, 2021
  

• Implement data augmentation by sliding window

  enhancement
  usadellab/Helixer#52 · Filter by author soi opened on May 11, 2021
  

• Extend validation of data

  usadellab/Helixer#42 · Filter by author alisandra opened on May 7, 2021
  1

• Benchmark compression alternatives

  usadellab/Helixer#40 · Filter by author alisandra opened on May 5, 2021
  1

• revive & test coverage as input

  usadellab/Helixer#33 · Filter by author alisandra opened on Feb 3, 2021

• Try reducing the learning rate again at some point

  experiment
  usadellab/Helixer#32 · Filter by author soi opened on Jan 14, 2021
  1

• Evaluate data augmentation that switches strands

  augmentationevaluation
  usadellab/Helixer#9 · Filter by author alisandra opened on Aug 27, 2020

• Add test for data augmentation that switches strands

  augmentationtesting
  usadellab/Helixer#8 · Filter by author alisandra opened on Aug 27, 2020