perturbation-metrics

To setup an appropriate python environment, simply install pertpy. This will also install other required packages such as scanpy and scvi-tools.

pip install pertpy

Simulations were run in R. To set up an appropriate R environment, please install the following in an R 4.0+ environment.

BiocManager::install("splatter")
BiocManager::install("scater")

Name		Name	Last commit message	Last commit date
Latest commit History 78 Commits
example_notebooks		example_notebooks
outputs		outputs
.gitignore		.gitignore
0_dataset_overview.ipynb		0_dataset_overview.ipynb
1_metric_runs_simulated.ipynb		1_metric_runs_simulated.ipynb
2_plotting_evaluation.ipynb		2_plotting_evaluation.ipynb
3_plotting_metric_bias.ipynb		3_plotting_metric_bias.ipynb
41_metric_bias_PDR.ipynb		41_metric_bias_PDR.ipynb
42_metric_bias_BioRep.ipynb		42_metric_bias_BioRep.ipynb
5_compare_lognorm_and_counts.ipynb		5_compare_lognorm_and_counts.ipynb
7_sensitivity_to_batch.ipynb		7_sensitivity_to_batch.ipynb
99_univariate_distances_as_DEG.ipynb		99_univariate_distances_as_DEG.ipynb
LICENSE		LICENSE
README.md		README.md
distance_result.py		distance_result.py
evaluate.py		evaluate.py
evaluation_util.py		evaluation_util.py
job_script_deg.sbatch		job_script_deg.sbatch
job_script_eval.sbatch		job_script_eval.sbatch
simulated_data.R		simulated_data.R
utils.py		utils.py

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