PDGrapher_evaluate

BMI702 project to understand and test PDGrapher on over-expression prediction
See branches in this repo for modifications applied to PDGrapher.

Name		Name	Last commit message	Last commit date
Latest commit History 15 Commits
CosmicCLP_MutantExport_only_verified_and_curated.csv		CosmicCLP_MutantExport_only_verified_and_curated.csv
OLD_download_tfatlas.sh		OLD_download_tfatlas.sh
OLD_extract_from_h5.py		OLD_extract_from_h5.py
OLD_process_biogrid_nx.py		OLD_process_biogrid_nx.py
OLD_process_npz_pt.py		OLD_process_npz_pt.py
README.md		README.md
additonal_analysis.ipynb		additonal_analysis.ipynb
baseline.ipynb		baseline.ipynb
compile_metrics_plot.py		compile_metrics_plot.py
create_splits_pert.py		create_splits_pert.py
evaluate_baseline.py		evaluate_baseline.py
evaluate_mod.py		evaluate_mod.py
export_lincs_oe_for_torch_geometric.py		export_lincs_oe_for_torch_geometric.py
export_lincs_xpr_for_torch_geometric.py		export_lincs_xpr_for_torch_geometric.py
generate_esm_embed.py		generate_esm_embed.py
master_pipeline.sh		master_pipeline.sh
n_folds_train_call.py		n_folds_train_call.py
pdgrapher_conda.yml		pdgrapher_conda.yml
ppi_all_genes_edgelist.txt		ppi_all_genes_edgelist.txt
prep_esm_embed.py		prep_esm_embed.py
process_lincs_healthy_npz.py		process_lincs_healthy_npz.py
process_lincs_pert_ctl_npz.py		process_lincs_pert_ctl_npz.py
report_4_22.ipynb		report_4_22.ipynb
run_experiments.sh		run_experiments.sh
scratchwork.ipynb		scratchwork.ipynb
scratchwork2.ipynb		scratchwork2.ipynb
train_calls.sh		train_calls.sh

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