aos

Data, analysis scripts and output of the analysis of the aos; regulation of autophagy in response to oxidative stress

Setting up the docker environment

The analysis was run on a docker image based on the the latest bioconductor/release_base2. 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/aos
$ docker run -it bcmslab/aos bash

Obtaining the source code

The source code is hosted publicly on this repository in a form of research compendium. This includes the functions used throughout the analysis as an R package, the scripts to run the analysis and finally the scripts to reproduce the figures and tables in this manuscript. From within the container, git can be used to cloned the source code. The cloned repository contains a sub-folder called analysis/scripts/ which can be used to reproduce the analysis from scratch

• get_data.R This scripts download several datasets from different sources in preparation of the analysis

• analysis.R This script loads the required libraries and runs all the steps of the analysis described in the manuscript

• figures/ A sub-folder with a separate file for each graph in the manuscript.

• tables/ A sub-folder with a sepearte file for each table in the manuscript.

The following code clones the repository containing the source code.

$ git clone http://github.com/BCMSLab/aos

Running the analysis

The analysis scripts is organized to be ran using a single make command. This will first load the necessary functions and run the main analysis and save the data in an R object data/aos_wgcna.rda. This will be used to generate the figures and graphs. In addition, a log file is generated in the sub-folder 'log/' for each script which can be used for troubleshooting.

To do that, the make command should be invoked from withing the analysis/ sub-folder.

$ cd aos/analysis/
$ make

Details of the R environment

The version of R that was used to perform this analysis is the 3.4.3 (2017-11-30) on x86\_64-pc-linux-gnu. The DESCRIPTION file in the main repository contains further details about the dependencies and the license of this work.

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