curated_perturbed_descriptor

Code for the Adipocyte paper (Curated gene expression dataset of differentiating 3T3-L1 adipocytes under pharmacological and genetic perturbations)

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/adiporeg_array:latest
$ docker run -it bcmslab/adiporeg_array: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 curated_perturbed_descriptor contains the scripts to download, prepare and analyze the data.

$ git clone https://github.com/BCMSLab/curated_perturbed_descriptor

Runing the analysis

In the directory curated_perturbed_descriptor, run make

$ cd curated_perturbed_descriptor
$ make all

Details of the R environment

The version of R that was used to perform this analysis is the 3.6.1 (2019-07-05) on x86_64-pc-linux-gnu.

More

This manuscript was published under the title Curated gene expression dataset of differentiating 3T3-L1 adipocytes under pharmacological and genetic perturbations