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A framework for survival prediction and analysis of ICGC datasets

Project description

Random Survival Forest

The ICGC-survival package provides an easy oppurtinity to perform survival prediction on ICGC datasets.


$ pip install icgc-survival


Getting Started

>>> from download_helper import login, download_file_by_project
>>> from feature_creator import extract_gene_affected_counts
>>> from label_creator import extract_survival_labels

>>> token = login(username, password)
>>> df = download_file_by_project(token=token, filetype="simple_somatic_mutation", release=28, project_code="ALL-US")
>>> ssm_gene_affected_counts = extract_gene_affected_counts(df)
>>> labels, features = extract_survival_labels(ssm_gene_affected_counts, donors)

>>> x, x_test, y, y_test = train_test_split(features, labels, shuffle=True, test_size=0.33, random_state=10)


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