nasiegel88 / 2023-clincal

Early-life gut microbiome development in rhesus monkeys

The data and code used in the analysis for the manuscript can be found in this repo.

• Complete blood counts
• Weight analysis

Steps to reproduce:

1. Clone this repo

git clone [email protected]:nasiegel88/2023-clinical.git
cd 2021-early-life-gut-microbiome

2. Create a repo2docker conda environment

It is assumed that conda (or mamba) and docker are installed on the system.

mamba create -n repo2docker -c conda-forge jupyter-repo2docker
conda activate repo2docker

3. Launch the notebook

This analysis involved a lot of packages thus it will take up to 20 minutes to build the docker image. Once the image is build select RStudio from the Jupyter Launcher.

jupyter-repo2docker --editable .

All output PDFs will be located within the documents directory.