caporaso-lab / office-microbes

Notebooks and code for our Sloan office microbiome project.

Office microbes

Notebooks and code for our Sloan office microbiome project (pre-print here, currently in press at mSystems).

The processed files used in these notebooks are available upon request (due to size, > 120GB). All raw data is publicly accessible in ERA under accession number ERP014651, and the processed files can all be computed from these raw files using QIIME 1.9.1.

To get started using this code

1. create a conda enviornment for the project: conda create -n office-microbes python=3.4 scikit-bio; source activate office-microbes
2. clone the repository: git clone [e-mail]:gregcaporaso/office-microbes.git
3. change to the resulting directory: cd office-microbes
4. run: pip install -e .
5. Change to the Final directory and launch the Jupyter notebook server with the command jupyter notebook