weberlab-hhu / Helixer

Using Deep Learning to predict gene annotations

weberlab-hhu/Helixer Issues

Question: How to find more smaller genes
Updated a month ago
How does helixer evaluate performance when predicting genomes?
Closed a month ago1
[Question] Can this be used broadly for all microeukaryotes (e.g., fungi, protists, etc)?
Updated a month ago8
When I run python Helixer.py, met: "ImportError: cannot import name 'where' from 'certifi' (unknown location"
Updated a month ago
OSError: [Errno 9] Bad file descriptor
Updated 2 months ago
sqlite3.DataError: string or blob too big
Updated 2 months ago
ModuleNotFoundError: No module named 'tensorflow.keras'
Updated 2 months ago1
nohup not helping in Helixer.py, run is stopped when connection is lost
Updated 2 months ago5
Helixer and the protein related domain
Closed 2 months ago1
gff3 specification
Updated 2 months ago1
Low busco scores for transcripts called on large Cupressus genome (10Gb) with helixer
Updated 2 months ago2
results from web tool not sent
Closed 2 months ago2
Some tensorflow warning/error messages when running Helixer via Singularity
Updated 2 months ago3
How to train the training models for non-listed species
Closed 5 months ago18
boolean index did not match indexed array along dimension 0
Updated 4 months ago
helixer_post_bin not correctly installed?
Closed 4 months ago15
please add a version option
Closed 4 months ago2
Fail early and clearly on fasta files with duplicate IDs
Updated 4 months ago
Online Version
Closed 4 months ago8
Issues with Gymnosperms
Closed 5 months ago2
Name the genes in order
Closed 5 months ago1
KeyError: 'Unable to open object (component not found)'
Closed 6 months ago2
Does Helixer produce multiple isoforms?
Closed 6 months ago2
Inference after training with RNAseq data
Closed 6 months ago6
KeyError: 'Unable to synchronously open object (component not found)' add_ngs_coverage.py
Closed 6 months ago6
Splitting up assemblies and running helixer
Closed 7 months ago5
Switch from h5 to native Keras models (or think about it)
Updated 7 months ago1
Segmentation fault (core dumped)
Closed 7 months ago7
Failed to add_ngs_coverage
Closed 10 months ago5
Training with RNAseq data failed
Closed a year ago4
Add Helixer to conda
Updated a year ago
Make --predict-phase not only the default but the only option.
Updated a year ago
helixer_post_bin does not work with trained models ( No "predictions_phase" on predictions.h5)
Closed a year ago1
Masked or non-masked genomes
Updated a year ago2
Question about the structure of HDF5 file
Closed a year ago2
change transition matrix to only include correct transitions from geenuff
Updated a year ago
record seed / random state
Updated 2 years ago
Clean up passing all the way and only having defaults in the wrong place for the write_by parameter
Updated 2 years ago1
animalia training file
Closed 2 years ago4
Optimize weighting of standard & phase loss and / or stop metric
Closed 2 years ago1
Helixer.py produces empty GFF file for very small Fasta Input
Closed 2 years ago1
Add metrics to fine tuning code
Closed 2 years ago
Run first fine tuning test
Closed 2 years ago
Run pretraining with large amount of data
Closed 2 years ago
Concatenate BERT outputs for one sequence and feed into LSTM
Closed 2 years ago1
Try relative positional embeddings
Closed 2 years ago1
Refactor redundancy between Sequence child classes into HelixerSequence
Updated 3 years ago
How to use helixer to annotate a genome in real world?
Closed 3 years ago6
Test for correct install
Updated 3 years ago
using --write-by during export failing on at least some genomes
Closed 3 years ago1