├── .github └── workflows │ └── test.yml ├── .gitignore ├── .gitmodules ├── LICENSE.txt ├── README.md ├── SSPS ├── Manifest.toml ├── Project.toml ├── precompile_script.jl ├── src │ ├── SSPS.jl │ ├── dbn_distributions.jl │ ├── dbn_models.jl │ ├── dbn_preprocess.jl │ ├── dbn_proposals.jl │ ├── mcmc_inference.jl │ └── state_updates.jl └── ssps_wrapper.jl ├── Snakefile ├── analysis_config.yaml ├── dream-challenge ├── prior │ ├── BT20.eda │ ├── BT549.eda │ ├── MCF7.eda │ └── UACC812.eda ├── test │ ├── TrueVec_BT20_EGF.csv │ ├── TrueVec_BT20_FGF1.csv │ ├── TrueVec_BT20_HGF.csv │ ├── TrueVec_BT20_IGF1.csv │ ├── TrueVec_BT20_Insulin.csv │ ├── TrueVec_BT20_NRG1.csv │ ├── TrueVec_BT20_PBS.csv │ ├── TrueVec_BT20_Serum.csv │ ├── TrueVec_BT549_EGF.csv │ ├── TrueVec_BT549_FGF1.csv │ ├── TrueVec_BT549_HGF.csv │ ├── TrueVec_BT549_IGF1.csv │ ├── TrueVec_BT549_Insulin.csv │ ├── TrueVec_BT549_NRG1.csv │ ├── TrueVec_BT549_PBS.csv │ ├── TrueVec_BT549_Serum.csv │ ├── TrueVec_MCF7_EGF.csv │ ├── TrueVec_MCF7_FGF1.csv │ ├── TrueVec_MCF7_HGF.csv │ ├── TrueVec_MCF7_IGF1.csv │ ├── TrueVec_MCF7_Insulin.csv │ ├── TrueVec_MCF7_NRG1.csv │ ├── TrueVec_MCF7_PBS.csv │ ├── TrueVec_MCF7_Serum.csv │ ├── TrueVec_UACC812_EGF.csv │ ├── TrueVec_UACC812_FGF1.csv │ ├── TrueVec_UACC812_HGF.csv │ ├── TrueVec_UACC812_IGF1.csv │ ├── TrueVec_UACC812_Insulin.csv │ ├── TrueVec_UACC812_NRG1.csv │ ├── TrueVec_UACC812_PBS.csv │ └── TrueVec_UACC812_Serum.csv └── train │ ├── BT20_main.csv │ ├── BT549_main.csv │ ├── MCF7_main.csv │ └── UACC812_main.csv ├── funchisq └── funchisq_wrapper.R ├── hill-method ├── dynamic_network_inference.m └── hill_dbn_wrapper.m ├── run_ssps ├── Snakefile ├── example_node_names.json ├── example_prior.csv ├── example_timeseries.csv └── ssps_config.yaml ├── scripts ├── changepoint_vec.jl ├── concatenate_samples.py ├── convergence_viz.py ├── dream_barchart.py ├── json_to_genie.py ├── lasso.jl ├── nested_data.jl ├── postprocess_samples.jl ├── preprocess_dream_prior.py ├── preprocess_dream_ts.py ├── prior_baseline.jl ├── score_dream.py ├── scoring.jl ├── script_util.py ├── sim_heatmap.py ├── simulate_data.jl ├── tabulate_mcmc_expense.py ├── tabulate_scores.py └── tabulate_timetest_results.py └── tests ├── baseline_predictions.genie ├── environment.yml └── ssps_csv.sh /.github/workflows/test.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gitter-lab/ssps/HEAD/.github/workflows/test.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gitter-lab/ssps/HEAD/.gitignore -------------------------------------------------------------------------------- /.gitmodules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gitter-lab/ssps/HEAD/.gitmodules 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