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

1. Exome
   R scripts to generate results for mutation load and clonal mutation load

2. Clonality_pre_post
   Scripts to analyze change in clonality of tumor pre and on therapy

3. RNASeq
   Scripts to analyze RNA-seq data

4. TCR
   Code to produce results regarding TCR analysis

5. Data
   Data from genomic pipelines (mutation calls, RNAseq matrix, etc)

6. Output
   All scripts save results to this directory

7. Packages
   Custom code/packages necessary to reproduce different portions of analysis