FunctionLab/selene
a framework for training sequence-level deep learning networks
Jupyter NotebookBSD-3-Clause-Clear
Issues
- 0
tangermeme backend
#197 opened by jmschrei - 1
Variant effect prediction REF mismatch
#187 opened by okurman - 1
pyfaidx.Fasta kwargs for sequences.Genome()?
#196 opened by mkarikom - 0
Is there a model fine-tuning function?
#195 opened by HanwenZhu98 - 0
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version update
#193 opened by FarmOmics - 0
New version Selene for PyTorch2.0.0?
#192 opened by jinyiliu1998 - 0
- 0
Loggers never close
#189 opened by rfriedman22 - 2
Support for other schedulers and early stopping
#183 opened by rfriedman22 - 2
Use Selene to predict variant effects genome-wide
#185 opened by andrewSharo - 1
- 0
model is suitable for classification?
#182 opened by Jasonxu0109 - 4
Slowdown of variant effect prediction with `torch.backends.cudnn.deterministic = True`
#180 opened by kathyxchen - 2
AnalyzeSequences bug due to Genome object
#178 opened by rfriedman22 - 2
- 0
MultiSampler missing test sampler in iterators
#166 opened by kathyxchen - 2
- 2
Support NN models with multiple inputs
#161 opened by sashuIya - 4
Prediction yaml file for Seqweaver
#157 opened by vagarwal87 - 0
Fix variable name for consistency with CLI configs
#154 opened by kathyxchen - 1
Documentation Formatting
#155 opened by mmingay - 0
Include CLI within the package
#152 opened by cthoyt - 4
Train and evaluate without `evalute_model` initialization in config does not work
#146 opened by kathyxchen - 1
In CASE1 Unresolved reference '_genomic_features' , Unresolved reference '_sequence'
#151 opened by yinuolb - 1
why I can't find the deepsea_TF_intervals.txt?
#150 opened by yinuolb - 0
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Hello,Is there an error in chromatin_profiles.tar.gz? ”tar: Error is not recoverable: exiting now“
#138 opened by Licko0909 - 0
`BASES_ARR` is initialized as a numpy array, but later changes to a Python list
#133 opened by aaronkw - 0
Problem with `BASES_ARR` changes persisting between lua model and non-lua model predictions
#130 opened by kathyxchen - 0
- 0
add parameter to append existing columns in VCF to output files in variant effect prediction
#129 opened by kathyxchen - 1
- 5
Fix YAML documentation for `metrics` configuration parameter in `train_model`
#125 opened by kathyxchen - 3
only support CUDA version <9.0.
#121 opened by carol007 - 0
MultiModelWrapper cannot be used on a GPU node
#122 opened by kathyxchen - 0
- 1
Argument type check in `_define_feature_thresholds implementation` in `GenomicFeatures` is too narrow
#106 opened by evancofer - 0
- 0
ReduceLROnPlateau in TrainModel uses incorrect mode
#115 opened by evancofer - 2
Questions about running case 2 on personal data.
#112 opened by kakorgao - 2
Not able to access nature article
#113 opened by arunpatala - 7
Naive question about evaluate
#108 opened by biomg - 2
Naive question about quickstart_training.ipynb
#107 opened by biomg - 0
- 2
Using protein sequences with Selene
#104 opened by ashishjain1988 - 3
Input files to process_data.sh missing (case 2)
#103 opened by ltorada