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weberlab-hhu
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Helixer
Using Deep Learning to predict gene annotations
GNU General Public License v3.0
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Add link to helixer-docker to README
#85
gglyptodon
closed
2 years ago
0
Enable Helixer.py execution from different directory and removal of duplicate test
#84
soi
closed
2 years ago
4
Helixer.py produces empty GFF file for very small Fasta Input
#83
soi
closed
1 year ago
1
minor readme extension
#82
soi
closed
2 years ago
1
animalia training file
#81
wyim-pgl
closed
1 year ago
4
Refactor redundancy between Sequence child classes into HelixerSequence
#80
alisandra
opened
2 years ago
0
How to use helixer to annotate a genome in real world?
#79
xiekunwhy
closed
2 years ago
6
add helixer.core to packages
#78
gglyptodon
closed
2 years ago
0
Update Readme and basic CI pipeline setup
#77
gglyptodon
closed
2 years ago
0
Test for correct install
#76
alisandra
opened
2 years ago
0
Try relative positional embeddings
#75
soi
closed
2 years ago
1
Concatenate BERT outputs for one sequence and feed into LSTM
#74
soi
closed
2 years ago
1
Run pretraining with large amount of data
#73
soi
closed
2 years ago
0
using --write-by during export failing on at least some genomes
#72
alisandra
closed
2 years ago
1
Run first fine tuning test
#71
soi
closed
2 years ago
0
Add metrics to fine tuning code
#70
soi
closed
2 years ago
0
Export data in kmer text form for pretraining
#69
soi
closed
2 years ago
0
Setup finetuning of pretrained model
#68
soi
closed
2 years ago
0
Pretrain BERT model
#67
soi
closed
2 years ago
0
phases (the three of them + None) do not always add to 1
#66
alisandra
closed
2 years ago
2
Bump tensorflow-gpu from 1.15.4 to 2.5.1
#65
dependabot[bot]
closed
2 years ago
1
dynamic species selection for training
#64
alisandra
closed
1 year ago
0
Evaluate new training datasets
#63
soi
opened
2 years ago
0
Rebuild training datasets from new single genomes
#62
soi
closed
2 years ago
0
Add config file to Geenuff
#61
soi
closed
2 years ago
0
Change UTR error generation in Geenuff
#60
soi
closed
2 years ago
0
Regenerate single genomes with multiple data changes
#59
soi
closed
2 years ago
1
Overlapping does not work with --chunk-size 19440
#58
soi
opened
3 years ago
1
Validate performance of new version of phytosome genomes
#57
soi
closed
3 years ago
0
Enable training of phase-only models
#56
soi
closed
3 years ago
1
Strands that don't have annotations do not get a seqid / start_ends
#55
soi
closed
3 years ago
1
Clean up / Rewrite exporter code
#54
soi
closed
3 years ago
0
Test (and probably bugfix) phase encoding where we don't start with phase 0
#53
alisandra
closed
3 years ago
5
Implement data augmentation by sliding window
#52
soi
opened
3 years ago
0
Test phase prediction with 6 classes output
#51
soi
closed
3 years ago
0
Test phase prediction with two distinct predictions
#50
soi
closed
3 years ago
0
Change model code for phase prediction
#49
soi
closed
3 years ago
0
Generate new dataset for plants with the phase info
#48
soi
closed
3 years ago
0
Import into Geenuff can show too high masked rate
#47
soi
closed
3 years ago
2
Test numerification of phases
#46
soi
closed
3 years ago
0
Add phases to numerification
#45
soi
closed
3 years ago
0
Remove option for non-one-hot encoding of labels
#44
soi
closed
3 years ago
1
Enable inference just from a fasta file
#43
soi
closed
3 years ago
1
Extend validation of data
#42
alisandra
opened
3 years ago
1
Add ability to filter by genome in visualization
#41
soi
closed
3 years ago
0
Benchmark compression alternatives
#40
alisandra
opened
3 years ago
1
Install things
#39
alisandra
closed
1 year ago
1
Check generalization with larger validation set after each training
#38
soi
closed
3 years ago
0
Make second larger cross genome validation set
#37
soi
closed
3 years ago
0
Numerify dna in parallel
#36
soi
closed
3 years ago
0
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