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Title: GitHub - FunctionLab/Seal: Sequence-to-expression transfer learning framework for context-specific prediction of variant effects on expression

Open Graph Title: GitHub - FunctionLab/Seal: Sequence-to-expression transfer learning framework for context-specific prediction of variant effects on expression

X Title: GitHub - FunctionLab/Seal: Sequence-to-expression transfer learning framework for context-specific prediction of variant effects on expression

Description: Sequence-to-expression transfer learning framework for context-specific prediction of variant effects on expression - GitHub - FunctionLab/Seal: Sequence-to-expression transfer learning framework for context-specific prediction of variant effects on expression

Open Graph Description: Sequence-to-expression transfer learning framework for context-specific prediction of variant effects on expression - GitHub - FunctionLab/Seal: Sequence-to-expression transfer learning framework ...

X Description: Sequence-to-expression transfer learning framework for context-specific prediction of variant effects on expression - GitHub - FunctionLab/Seal: Sequence-to-expression transfer learning framework ...

Mail addresses
yhao@flatironinstitute.org

Opengraph URL: https://github.com/FunctionLab/Seal

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download_resources.shhttps://github.com/FunctionLab/Seal/blob/main/download_resources.sh
download_resources.shhttps://github.com/FunctionLab/Seal/blob/main/download_resources.sh
requirements.txthttps://github.com/FunctionLab/Seal/blob/main/requirements.txt
requirements.txthttps://github.com/FunctionLab/Seal/blob/main/requirements.txt
seal_interpret.pyhttps://github.com/FunctionLab/Seal/blob/main/seal_interpret.py
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Seal modelhttps://doi.org/10.5281/zenodo.14104608
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https://github.com/FunctionLab/Seal#usage
https://github.com/FunctionLab/Seal#context-specific-prediction-of-variant-effects-on-expression
example bash scripthttps://github.com/FunctionLab/Seal/blob/main/test/predict/test_var_predict.sh
examplehttps://github.com/FunctionLab/Seal/blob/main/test/predict/test_var.vcf
examplehttps://github.com/FunctionLab/Seal/blob/main/model/tissue_state_early_fetal_to_adult/tissue_state_early_fetal_to_adult_seal_model_summary.txt
examplehttps://github.com/FunctionLab/Seal/blob/main/test/predict/test_var_tissue_state_effect_pred.tsv
model info filehttps://github.com/FunctionLab/Seal/blob/main/model/tissue_state_early_fetal_to_adult/tissue_state_early_fetal_to_adult_seal_model_summary.txt
model info filehttps://github.com/FunctionLab/Seal/blob/main/model/cell_state_early_fetal/cell_state_early_fetal_seal_model_summary.txt
model info filehttps://github.com/FunctionLab/Seal/blob/main/model/cell_state_mid_fetal_to_adult/cell_state_mid_fetal_to_adult_seal_model_summary.txt
the annotation filehttps://github.com/FunctionLab/Seal/blob/main/resource/cell_state_annotation.xlsx
UCSC lift genome annotationshttps://genome.ucsc.edu/cgi-bin/hgLiftOver
https://github.com/FunctionLab/Seal#training-a-sequence-to-expression-transfer-learning-model-from-scratch
example bash scripthttps://github.com/FunctionLab/Seal/blob/main/test/train/test_train_from_scratch.sh
examplehttps://github.com/FunctionLab/Seal/blob/main/resource/geneanno.exp.csv_general_brain.tsv
examplehttps://github.com/FunctionLab/Seal/blob/main/resource/brain_dev_exp_tissue_group.tsv
https://github.com/FunctionLab/Seal#fine-tuning-a-pre-trained-model-for-predicting-gene-expression-under-specific-contexts
example bash scripthttps://github.com/FunctionLab/Seal/blob/main/test/train/test_train_from_pretrained.sh
https://github.com/FunctionLab/Seal#interpreting-trained-transfer-learning-model-to-compute-attribution-scores-of-chromatin-features
example bash scripthttps://github.com/FunctionLab/Seal/blob/main/test/interpret/test_var_interpret.sh
examplehttps://github.com/FunctionLab/Seal/blob/main/test/predict/test_var.vcf
examplehttps://github.com/FunctionLab/Seal/blob/main/model/tissue_state_early_fetal_to_adult/tissue_state_early_fetal_to_adult_seal_model_summary.txt
examplehttps://github.com/FunctionLab/Seal/blob/main/test/interpret/test_var_tissue_state_early_fetal_to_adult_deeplift_attribution_score_outcome_0.npy
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