shaikh-sears-clin-cancer-research-2021

This repository is intended to served as a resource with supporting statistical code and processed microbiome data from Shaikh et al. (2021, Clinical Cancer Research) "A uniform computational approach improved on existing pipelines to reveal microbiome biomarkers of non-response to immune checkpoint inhibitors."

• Top-level directory: shaikh-sears-clin-cancer-research-2021/

./shaikh-sears-clin-cancer-research-2021/
├── README.md  <-- this readme file
├── code      
│   ├── A01-merge-profiles-across-studies.pl <-- merges WGS and 16S rRNA profiles from the data/processed directory
│   ├── A02-meta-analysis-forest-plots.pl    <-- random effects modeling + forest plots for species and PICRUSt features (figure 2, and supplementary figs)
│   ├── A03-compile-indicator-taxa.pl        <-- compilation of indicator taxa derived from A02 and metadata
│   ├── figure03.pl  <-- elements of fig 3 from Shaikh et al.
│   ├── figure04.r   <-- elements of fig 4 from Shaikh et al.
│   ├── figure05.r   <-- elements of fig 5 from Shaikh et al.
│   └── figureS1.r   <-- elements of fig S1 from Shaikh et al.
├── analysis         <-- outputs generated by scripts in code/
│   ├── A01-merge-profiles-across-studies
│   ├── A02-meta-analysis-forest-plots
│   ├── A03-compile-indicator-taxa
│   ├── figure03
│   ├── figure04
│   ├── figure05
│   └── figureS1
└── data            <-- contains WGS Metaphlan2 profiles and Resphera Insight 16S rRNA profiles per study
    ├── final
    │   ├── metadata.2019-04-22.txt
    │   ├── pre-E01 <-- input data for validation cohorts
    │   └── pre-S1  <-- input data for paired WGS/16S rRNA correlation analysis (figure S1)
    └── processed <-- contains metadata / WGS Metaphlan2 profiles / Resphera Insight 16S rRNA profiles / PICRUSt functional profiles per study
         ├── Chaput.2017
         │   ├── 16SrRNA
         │   └── Metadata
         ├── Frankel.2017
         │   ├── 16SrRNA
         │   ├── METADATA
         │   └── WGS
         ├── Gopalakrishnan.2017
         │   ├── 16SrRNA
         │   ├── METADATA
         │   └── WGS
         ├── Matson.2018
         │   ├── 16SrRNA
         │   ├── METADATA
         │   └── WGS
         ├── Routy.2017
         │   ├── 16SrRNA
         │   ├── METADATA
         │   └── WGS
         ├── Peters.2019
         │   ├── 16SrRNA
         │   └── METADATA         
         ├── Hakozaki.2020  <-- (aka Richard et al.)
         │   ├── 16SrRNA
         │   └── METADATA
         └── Zheng.2019
             ├── SRA
             └── WGS

Authors

• James Robert White PhD - Initial work - GitHub