weberlab-hhu Helixer issues

weberlab-hhu / Helixer

Using Deep Learning to predict gene annotations

GNU General Public License v3.0

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issues

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Question: How to find more smaller genes

#135 srobb1 opened 17 hours ago
0
When I run python Helixer.py, met: "ImportError: cannot import name 'where' from 'certifi' (unknown location"

#134 kuangzhuoran opened 1 week ago
0
OSError: [Errno 9] Bad file descriptor

#133 ZhangPY-bioinformatics opened 3 weeks ago
0
sqlite3.DataError: string or blob too big

#132 arslan9732 opened 3 weeks ago
0
How does helixer evaluate performance when predicting genomes?

#131 ZhangPY-bioinformatics closed 1 week ago
1
ModuleNotFoundError: No module named 'tensorflow.keras'

#130 xiekunwhy opened 3 weeks ago
1
Helixer and the protein related domain

#129 LeoVincenzi closed 1 month ago
1
nohup not helping in Helixer.py, run is stopped when connection is lost

#128 alexandrosbousios opened 1 month ago
5
gff3 specification

#127 nhartwic opened 1 month ago
1
Low busco scores for transcripts called on large Cupressus genome (10Gb) with helixer

#126 Bios4Biol opened 2 months ago
2
boolean index did not match indexed array along dimension 0

#125 Wenfei-Xian opened 2 months ago
0
results from web tool not sent

#124 jasonwjohns closed 1 month ago
2
Some tensorflow warning/error messages when running Helixer via Singularity

#123 spoonbender76 opened 2 months ago
3
fixed typo in download message

#122 gglyptodon closed 3 months ago
0
installation improvements and version

#121 alisandra closed 3 months ago
0
Fail early and clearly on fasta files with duplicate IDs

#120 alisandra opened 3 months ago
0
Online Version

#119 LeoVincenzi closed 3 months ago
8
Issues with Gymnosperms

#118 nhartwic closed 3 months ago
2
Name the genes in order

#117 yangfangyuan0102 closed 3 months ago
1
helixer_post_bin not correctly installed?

#116 LeoVincenzi closed 3 months ago
15
KeyError: 'Unable to open object (component not found)'

#115 ply2022 closed 4 months ago
2
Does Helixer produce multiple isoforms?

#114 Laura-CE-Campbell closed 5 months ago
2
How to train the training models for non-listed species

#113 JiantaoZhao426 closed 3 months ago
18
KeyError: 'Unable to synchronously open object (component not found)' add_ngs_coverage.py

#112 arslan9732 closed 5 months ago
6
Inference after training with RNAseq data

#111 hjjansen closed 5 months ago
6
Splitting up assemblies and running helixer

#110 Toffeeladd closed 5 months ago
5
Segmentation fault (core dumped)

#109 qussai96 closed 6 months ago
7
please add a version option

#108 colindaven closed 3 months ago
2
minor_things_inference

#107 soi closed 3 months ago
0
Failed to add_ngs_coverage

#106 EdgarLW closed 8 months ago
5
Training with RNAseq data failed

#105 MartinPippel closed 10 months ago
4
Add Helixer to conda

#104 xiekunwhy opened 11 months ago
0
Make --predict-phase not only the default but the only option.

#103 alisandra opened 11 months ago
0
Switch from h5 to native Keras models (or think about it)

#102 alisandra opened 11 months ago
1
helixer_post_bin does not work with trained models ( No "predictions_phase" on predictions.h5)

#101 piroyon closed 11 months ago
1
[Question] Can this be used broadly for all microeukaryotes (e.g., fungi, protists, etc)?

#100 jolespin opened 1 year ago
8
Masked or non-masked genomes

#99 GoliczGenomeLab opened 1 year ago
2
Question about the structure of HDF5 file

#98 ShanshanGu533 closed 1 year ago
2
Bump tensorflow from 2.10.0 to 2.11.1

#97 dependabot[bot] opened 1 year ago
0
Bump werkzeug from 2.2.2 to 2.2.3

#96 dependabot[bot] opened 1 year ago
0
update dustdas version

#95 gglyptodon closed 1 year ago
0
Bump tensorflow from 2.10.0 to 2.10.1

#94 dependabot[bot] closed 1 year ago
1
Bump future from 0.18.2 to 0.18.3

#93 dependabot[bot] opened 1 year ago
0
Bump certifi from 2022.9.24 to 2022.12.7

#92 dependabot[bot] opened 1 year ago
0
Bump ipython from 8.6.0 to 8.10.0

#91 dependabot[bot] opened 1 year ago
0
change transition matrix to only include correct transitions from geenuff

#90 alisandra opened 1 year ago
0
record seed / random state

#89 alisandra opened 1 year ago
0
Update README.md

#88 BjoernUsadel closed 1 year ago
0
Clean up passing all the way and only having defaults in the wrong place for the write_by parameter

#87 alisandra opened 1 year ago
1
Optimize weighting of standard & phase loss and / or stop metric

#86 alisandra closed 1 year ago
1