Analysis Notebooks and Code for The American Gut Project

ipynb contains executable Jupyter notebooks.

ipynb/env describe the conda and run enviroments associated with these notebooks.

non-ipynb contains analyses performed outside of Jupyter notebooks.

Manuscript

The manuscript associated with this repository is open access and published under mSystems. If code from this repository or data from the American Gut are used, please consider citing this manuscript.

Data access

Data for the American Gut Project can be accessed in a few ways and are described in brief below. This is a living project, so these datasets will continue to grow with the exception of the fixed datasets. The fixed datasets correspond to what was used for the manuscript.

• all sequence and metadata are in EBI under the project PRJEB11419. This dataset is not fixed.
• all sequence, metadata and processed summaries can be obtained from Qiita under study ID 10317. This dataset is not fixed.
• the 16S and metadata can be obtained by querying redbiom using qiita_study_id==10317. This dataset is not fixed.
• the 16S data in BIOM-Format and metadata used in the manuscript from the public anonymous microbio.me FTP. This dataset is fixed and will not change.

The metabolomics datasets are housed in [GNPS[(http://gnps.ucsd.edu/). The datasets listed below are fixed. Additional metabolomics data from the American Gut will be available in GNPS in the future.

• the antibiotic subset
• the number of types of plants subset
• the cell culture supernatant
• the co-networked fecal samples