Skip to content

README.md

Latest commit

 

History

History
32 lines (28 loc) · 1.36 KB

README.md

File metadata and controls

32 lines (28 loc) · 1.36 KB

sci2017_analysis

Data and analysis codes for Matson et al. 2017 manuscript The commensal microbiome is associated with anti-PD-1 efficacy in metastatic melanoma patients. Please refer to READMEs in Data and Notebook sub-directory for more detailed information of the files. Description of how the OTU and shotgun species abundance tables are generated from raw FastQ files are provided in the supplementary methods section of the manuscript.

Contents

  • Data
    Processed biom or csv data files used in 16S, shotgun, and qPCR analyses.

    • human_16S.sampleinfo.csv
    • human_16S.even13190.abs.sig.csv
    • human_16S.even13190.rel.sig.csv
    • human_16S.even13190.stats.sig.csv
    • human_16S.even13190.abs.full.biom
    • human_16S.even13190.rel.full.biom
    • human_16S_qPCR.csv
    • human_shotgun.rel.full.csv
    • human_joint_evidence.csv
    • mouse_16S.sampleinfo.csv
    • mouse_16S.even22560.abs.sig.csv
    • mouse_16S.even22560.rel.sig.csv
    • mouse_16S.even22560.abs.full.biom
    • mouse_16S.even22560.rel.full.biom

  • Notebook
    Jupyter notebooks that provide custom codes and input/output to reproduce relevant portion of analysis.

    • 01_OTU_heatmap.ipynb
    • 02_qPCR_score.ipynb
    • 03_OTU_ratio.ipynb
    • 04_16S_shotgun_cor.ipynb
    • 05_Joint_evidence.ipynb
    • assets