README.md

obese_mice

Code for the data descriptor paper (Tissue-specific gene expression in obese hyperglycemic mice)

Setting up the docker environment

The analysis was run on a docker image based on the the latest rocker/verse. Other R packages were added to the image and were made available as an image that can be obtained and launched on any local machine running docker.

docker pull bcmslab/obsesmice:latest
docker run -it bcmslab/obsesmice:latest bash

Alternatively, the image can be built locally form the provided Docerfile. Pass docker/Dockerfile to the docker build command.

Obtaining the source code

The source code is hosted publicly on this repository in the form of a research compendium. This includes the scripts to reproduce the figures and tables in this manuscript.

git clone https://github.com/MahShaaban/obese_mice

Runing the analysis

In the directory obese_mice, run make

cd curated_adipo_descriptor
make all

This file contains the recipes to generate several rds objects in data and tables and figures in manuscript/.