bms038 analysis
Data and associated code to perform analysis in manuscript "Tumor and Microenvironment Evolution during Immune Checkpoint Blockade Therapy with Nivolumab". Each sub-directory contains code to reproduce relevant portion of analysis. See READMEs in each sub-directory for additional details. Description of how the mutation list and RNAseq count matrix are generated from raw BAM files are provided in the methods section of the manuscript.
Contents
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Exome
R scripts to generate results for mutation load and clonal mutation load -
Clonality_pre_post
Scripts to analyze change in clonality of tumor pre and on therapy -
RNASeq
Scripts to analyze RNA-seq data -
TCR
Code to produce results regarding TCR analysis -
Data
Data from genomic pipelines (mutation calls, RNAseq matrix, etc) -
Output
All scripts save results to this directory -
Packages
Custom code/packages necessary to reproduce different portions of analysis