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Clinical_Covariates.ipynb
HNSCC_clinical_characterization.ipynb Pre-package split. Oct 12, 2014
HNSCC_figures.ipynb Pre-package split. Oct 12, 2014
HPV_Process_Data.ipynb Pre-package split. Oct 12, 2014
HPV_characterization.ipynb
Imports.ipynb
Index.ipynb
Molecular_Validation.ipynb
Multivariate_Modeling.ipynb Pre-package split. Oct 12, 2014
NotebookImport.py Implement MinRK's notebook import code. May 8, 2014
PANCAN_cohort.ipynb
Prognostic_Screen.ipynb
README.ipynb Pre-package split. Oct 12, 2014
README.md Fix headers Sep 6, 2017
Reviewer_Response.ipynb Pre-package split. Oct 12, 2014
Secondary_Screen.ipynb Pre-package split. Oct 12, 2014
TP53_3p_Confounding.ipynb Split out interaction analysis from Reviewer Response. Jul 16, 2014
TP53_3p_Interaction.ipynb
TP53_exploration.ipynb Pre-package split. Oct 12, 2014
UPMC_cohort.ipynb Pre-package split. Oct 12, 2014
binarize_clinical.ipynb Pre-package split. Oct 12, 2014
copy_number_exploration.ipynb
download_data.ipynb Pre-package split. Oct 12, 2014
get_all_MAFs.ipynb
get_updated_clinical.ipynb Pre-package split. Oct 12, 2014
muTect_streamline.ipynb Clean up for publication. Mar 26, 2014
new_data_process_TP53_Pancancer.ipynb Clean up for publication. Mar 26, 2014

README.md

Guide to Running

Initialization

  • download_data (nbviewer) Pulls all of the necessary data from the net and constructs the file tree and data objects used in the rest of the analysis.

  • get_all_MAFs (nbviewer) Script to download and process updated MAF files from the TCGA Data Portal.

  • get_updated_clinical (nbviewer) Script to download and process updated clinical data from the TCGA Data Portal.

Primary Analysis

(There are dependencies among these, run them in order.)

  • HPV_Process_Data (nbviewer) Compile HPV status for all patient tumors.
    Calculate global variables and meta features in the HPV- background.

  • binarize_clinical (nbviewer) Process clinical variables into binary matrix for use in prognostic screens.

  • Prognostic_Screen (nbviewer) Run the primary prognostic screen for HPV- HNSCC patients.

  • Secondary_Screen (nbviewer) Run the prognostic screen for HPV- HNSCC patients with the TP53-3p event.

  • HNSCC_figures (nbviewer) Generate some of the figure panels for the HNSCC discovery cohort. Some of the other figures and figure panels are generated inline with analysis.

Validation Cohorts

Targeted Analysis for Support of Main Findings

Variant Calling (optional)

This requires a number of additional dependencies for sequencing analysis and as well as function calls to proprietary software installed on our virtual machine hosed by Annai Systems. We have included all of the dependencies of this mutation calling step in the supplement as MAF files and highly recomend starting with these as opposed to recalling mutations.

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