hammerlab/paper-aocs-chemo-neoantigens

Name: paper-aocs-chemo-neoantigens

Owner: Hammer Lab

Description: Manuscript on chemotherapy-induced neoantigens in samples from the Australian Ovarian Cancer Study

Created: 2016-04-23 21:19:05.0

Updated: 2016-11-29 00:10:11.0

Pushed: 2017-11-28 20:40:22.0

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Size: 597829

Language: Jupyter Notebook

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README

paper-201604

This repository has the notebooks, LaTeX source, data, figures, and supplemental files for the article “Chemotherapy weakly contributes to predicted neoantigen expression in ovarian cancer”.

Running the analyses

Analyses were run in this order.

• 'samples' notebook
• scripts/annotate_variants.sh
• 'prepare and merge varlens annotated mutations' notebook
• 'neoantigen and mutation counts' notebook
• 'signature extractions with model' notebook
• 'prepare mutation counts for deconstructsigs' notebook
• R script: R/signature_deconstruction.R
• 'deconstructSigs results' notebook
• 'signature probabilities per mutation' notebook
• 'plot mutation and neoantigen signature sources' notebook
• 'plot extracted signatures'
• 'prepare additional files'