Skip to content

lorcanpd/readformer

BranchesTags

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

215 Commits
components
components
 
 
Dockerfile
Dockerfile
 
 
README.md
README.md
 
 
adv_pretraining.py
adv_pretraining.py
 
 
analyse_predictions.py
analyse_predictions.py
 
 
construct_finetuning_data.py
construct_finetuning_data.py
 
 
coverage_to_bed.py
coverage_to_bed.py
 
 
create_k_folds.py
create_k_folds.py
 
 
estimate_memory_reqs.sh
estimate_memory_reqs.sh
 
 
finetune.py
finetune.py
 
 
get_artefact_reads.py
get_artefact_reads.py
 
 
get_candidate_reads.py
get_candidate_reads.py
 
 
get_mutation_reads.py
get_mutation_reads.py
 
 
get_training_reads.py
get_training_reads.py
 
 
get_validation_batch.py
get_validation_batch.py
 
 
main.py
main.py
 
 
memory_requirements.py
memory_requirements.py
 
 
mlm_pretraining.py
mlm_pretraining.py
 
 
predict.py
predict.py
 
 
predict_on_test_set.py
predict_on_test_set.py
 
 
pretrain_readwise_only.py
pretrain_readwise_only.py
 
 
run_empirical_bayes.py
run_empirical_bayes.py
 
 
submit_empirical_bayes_no_pretrain.sh
submit_empirical_bayes_no_pretrain.sh
 
 
submit_finetuning_for_pretrained.sh
submit_finetuning_for_pretrained.sh
 
 
submit_finetuning_no_pretrain.sh
submit_finetuning_no_pretrain.sh
 
 
submit_predict_on_test_no_pretrain.sh
submit_predict_on_test_no_pretrain.sh
 
 
submit_pretraining.sh
submit_pretraining.sh
 
 
submit_readwise_pretrain.sh
submit_readwise_pretrain.sh
 
 

Repository files navigation

In development

██╗  ██╗  █████╗██╗ ████▒█▒███████╗ ██████╗ ██╗  ████╗███▒███╗░█╗  ██╗██╗  ██╗██╗██╗
╚═╝  ╚═╝  ╚════╝╚═╝ ╚═════════════╝ ╚═════╝ ╚═╝  ╚═══╝╚══════╝╚═╝  ╚═╝╚═╝  ╚═╝╚═╝╚═╝
██████╗ ███████╗ █░███╗ ██████╗ █▒█▒███╗ ██████╗ ███▒██╗ ███╗   ███╗███████╗██████╗ 
█▒╔══██╗██╔════╝██╔══██╗▒█╔══██╗██╔════╝██╔═══██╗██╔══██╗▒███╗ ████║██╔════╝██╔══██╗
█▒███░╔╝██░██╗  ██░████║▒█║  ██║███▒█╗  ██║   ██║███▒██╔╝██╔██░█╔██║█▒▒██╗  ██████╔╝
█▒╔══░█╗██╔══╝  ██╔══██║██║  ██║██╔══╝  ██║   ██║██╔══██╗██║╚█░╔╝██║██╔══╝  ██╔══██╗
██║  ▒█║███████╗██║  ██║▒█████╔╝█▒║     ╚██████╔╝██║  ██║▒█║ ╚═╝ ██║█▒▒████╗██║  ██║
╚═╝  ╚═╝╚══════╝╚═╝  ╚═╝╚═════╝ ╚═╝      ╚═════╝ ╚═╝  ╚═╝╚═╝     ╚═╝╚══════╝╚═╝  ╚═╝
░██████░██░████████▒█▒███████████▒█▒█╗  ██████░██░████████▒█▒█████████████╗   ██████╗
████╔░████░█╔██╔══██╗██╔══██╗██╗██╔══██╔══██╔══█████╔██╔═════█░╔═██████╔═██████╔═██╔╝
╚═══╝╚══════╝╚═╝  ╚═╝╚═╝  ╚═╝╚═╝╚═╝  ╚═╝  ╚═╝  ╚════╝╚═╝     ╚═╝ ╚═════╝ ╚═════╝ ╚═╝
A transformer-based architecture for calling somatic mutations from aligned reads.

About

No description, website, or topics provided.

Resources

Readme
Activity

Stars

0 stars

Watchers

1 watching

Forks

0 forks
Report repository

Releases

No releases published

Packages

 
 
 

Contributors

Languages