cregart

A manuscript about the cRegulome R package which is part of the rOpenSci now.

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/cregart:20181219
$ docker run -it bcmslab/cregart:20181219 bash

Obtaining the source code

The source code is hosted publicly on this repository in a form of research compendium. This includes the scripts to reproduce the figures and tables in this manuscript. From within the container, git can be used to clone the source code.

The following code clones the repository containing the source code.

$ git clone http://github.com/MahShaaban/cregart

Running the analysis

The analysis scripts is organized to be ran using a single make command. This will first extract and save the data in R objects. This will be used to generate the figures and tables. 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 within the cloned repo.

$ cd cregart
$ make

Details of the R environment

The version of R that was used to perform this analysis is the 3.5.0 (2018-04-23) 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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