mbur-sequence-learning

Exploring sequence2function relationships in M. buryatense promoter regions using deep learning methods

Name		Name	Last commit message	Last commit date
Latest commit History 47 Commits
alt_out		alt_out
config		config
data		data
img		img
out_mpra_reduction		out_mpra_reduction
out_synth_cls		out_synth_cls
saved_models		saved_models
.gitattributes		.gitattributes
.gitignore		.gitignore
5G_ups_vs_cds_cls.ipynb		5G_ups_vs_cds_cls.ipynb
5org_cls.ipynb		5org_cls.ipynb
README.md		README.md
cu_prediction_splitPrep_coldStart.ipynb		cu_prediction_splitPrep_coldStart.ipynb
cuperus_random_utr_prediction.ipynb		cuperus_random_utr_prediction.ipynb
evo_reduction.py		evo_reduction.py
evo_reduction_arch_compare_hyak.ipynb		evo_reduction_arch_compare_hyak.ipynb
evolution_mpra.ipynb		evolution_mpra.ipynb
extract_seqs_from_org_genbanks.ipynb		extract_seqs_from_org_genbanks.ipynb
genbank_utils.py		genbank_utils.py
license		license
models.py		models.py
mpra_reduction.py		mpra_reduction.py
ncbi_jgi_aln.ipynb		ncbi_jgi_aln.ipynb
override.py		override.py
pretraining_cu_performance_comparison.ipynb		pretraining_cu_performance_comparison.ipynb
pretraining_cu_prediction.ipynb		pretraining_cu_prediction.ipynb
pretraining_cu_prediction_vaishnav.ipynb		pretraining_cu_prediction_vaishnav.ipynb
pytorchtools.py		pytorchtools.py
synth_classification_randomseqs.py		synth_classification_randomseqs.py
synthetic_DNAclassification_task1_simple.ipynb		synthetic_DNAclassification_task1_simple.ipynb
synthetic_DNAclassification_task2_harder.ipynb		synthetic_DNAclassification_task2_harder.ipynb
torch_utils.py		torch_utils.py
utils.py		utils.py
viz.py		viz.py

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