This repository contains the Dockerfile that reproduces the figures and results for the Cell-line analysis from the following paper:
A Transcriptional Signature for TGFβ-induced EMT in Cancer
Momeneh Foroutan, Joseph Cursons, Soroor Hediyeh-Zadeh, Erik W. Thompson and Melissa J. Davis
Download and install Docker. Start Docker and run the following command:
docker run -p 49000:8787 -d davislaboratory/mforoutan_tgfb_2017_celllines
(You can replace 49000 with another open port if you want.) Navigate in your web browser to
http://0.0.0.0:49000. This will open up rstudio. The username and password are both davislab.
You can run generate_all_experiments.R to reproduce all the figures and results from Foroutan et al.
# In rstudio run:
source("generate_all_experiments.R")
If you are running on a Mac, you should have already installed either Docker for Mac, or Docker Toolbox. Instructions are the same as above if you're using Docker for Mac. However, if you're using Docker Toolbox you would need to replace "0.0.0.0" with your IP address. You're IP address is displayed once you run the Docker Quick Terminal from Docker Toolbox.Then navigate in the browser to $IP:49000.
Please note that some of the scripts provided with the image perform computationally intensive operations. Our testings suggest that Mac users running Docker Toolbox will have difficulties running some of the scripts due to CPU limitations of Virtualbox-based Docker machines. Users are, therefore, strongly encouraged to install and run Docker for Mac.
Please contact Soroor (hediyehzadeh.s@wehi.edu.au) for bug reports or help requests, or simply open an issue.