Data, analysis scripts and output of the analysis of the RKIP, autophagy and EMT coexpression in developing prostate cancer.
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/rkip $ docker run -it bcmslab/rkip 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.RThis scripts download several datasets from different sources in preparation of the analysis
analysis.RThis 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/rkip
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/rkip_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
$ cd rkip/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
DESCRIPTION file in the main repository contains further details about the dependencies and the license of this work.
- Published paper, here