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30 Open 103 Closed
30 Open 103 Closed
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Issues list

Singularity image missing dependency?
#167 opened Dec 18, 2024 by Artifice120
1
over-prediction small contigs enhancement New feature or request evaluation performance
#147 opened Oct 30, 2024 by mhooykaas
4
Micro exons with single bases or two enhancement New feature or request evaluation performance
#138 opened Jul 31, 2024 by ke-shi
3
Question: How to find more smaller genes
#135 opened Jul 2, 2024 by srobb1
2
When I run python Helixer.py, met: "ImportError: cannot import name 'where' from 'certifi' (unknown location"
#134 opened Jun 20, 2024 by kuangzhuoran
1
sqlite3.DataError: string or blob too big data format
#132 opened Jun 9, 2024 by arslan9732
@felicitas215
2
gff3 specification data format
#127 opened May 10, 2024 by nhartwic v0.3.5
1
Low busco scores for transcripts called on large Cupressus genome (10Gb) with helixer enhancement New feature or request
#126 opened Apr 19, 2024 by Bios4Biol
2
Some tensorflow warning/error messages when running Helixer via Singularity
#123 opened Apr 11, 2024 by spoonbender76
3
Fail early and clearly on fasta files with duplicate IDs usability
#120 opened Mar 22, 2024 by alisandra
@alisandra @felicitas215
Add Helixer to conda
#104 opened Jul 19, 2023 by xiekunwhy
Make --predict-phase not only the default but the only option. usability
#103 opened Jul 16, 2023 by alisandra
@felicitas215
[Question] Can this be used broadly for all microeukaryotes (e.g., fungi, protists, etc)?
#100 opened Jun 3, 2023 by jolespin
8
Masked or non-masked genomes
#99 opened May 30, 2023 by GoliczGenomeLab
2
change transition matrix to only include correct transitions from geenuff
#90 opened Feb 2, 2023 by alisandra
record seed / random state enhancement New feature or request
#89 opened Jan 24, 2023 by alisandra
@felicitas215
Clean up passing all the way and only having defaults in the wrong place for the write_by parameter
#87 opened Jan 4, 2023 by alisandra
1
Refactor redundancy between Sequence child classes into HelixerSequence clean up
#80 opened Jan 12, 2022 by alisandra
@alisandra
Test for correct install usability
#76 opened Nov 30, 2021 by alisandra
Evaluate new training datasets enhancement New feature or request
#63 opened Jul 22, 2021 by soi
@soi
Implement data augmentation by sliding window enhancement New feature or request
#52 opened May 11, 2021 by soi
@soi
Extend validation of data
#42 opened May 7, 2021 by alisandra
1
Benchmark compression alternatives
#40 opened May 5, 2021 by alisandra
1
revive & test coverage as input
#33 opened Feb 3, 2021 by alisandra
Try reducing the learning rate again at some point experiment
#32 opened Jan 14, 2021 by soi
1
ProTip! Exclude everything labeled bug with -label:bug.