README.md

auto_adipo_diff

Code for the Cells paper (Transcriptional Regulation of Autophagy Genes via Stage-Specific Activation of CEBPB and PPARG during Adipogenesis)

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/autoreg:latest
$ docker run -it bcmslab/autoreg:latest bash

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. Another public repository autoreg contains the scripts to download, prepare and analyze the data. From within the container, git can be used to clone the source code using the --recurse-submodules flag to include the submodules.

The following code clones the repository containing the source code.

$ git clone --recurse-submodules http://github.com/BCMSLab/auto_adipo_diff

Runing the analysis

In the submodule autoreg, run make

$ cd auto_adipo_diff/autoreg
$ make analysis

Generating figures and tables

The script to generate the figures and tables in the manuscirpt can be als ran through make

$ cd auto_adipo_diff
$ make all

Details of the R environment

The version of R that was used to perform this analysis is the 3.7.0 (2019-04-07) on x86\_64-pc-linux-gnu.

More

This manuscript was published under the title Transcriptional Regulation of Autophagy Genes via Stage-Specific Activation of CEBPB and PPARG during Adipogenesis: A Systematic Study Using Public Gene Expression and Transcription Factor Binding Datasets