/bms038_analysis

Code and additional processed data for manuscript "Tumor and Microenvironment Evolution during Immunotherapy with Nivolumab"; see for manuscript https://doi.org/10.1016/j.cell.2017.09.028 See also http://www.ioexplorer.org for interactive visuallization

Primary LanguagePython

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