Public | Automated Build

Last pushed: 6 days ago
Short Description
Based on rocker/rstudio with R Studio server and bioconductor packages
Full Description

<img alt="Docker" src="https://msopentech.com/wp-content/uploads/dockericon.png" width="200">
<img alt="R-Studio" src="https://teespring-storecontent.s3.amazonaws.com/FW6s2ljYB6HuZgDe15SiOQ_store_header_image" width="200">
<img alt="Bioconductor" src="https://bioconductor.org/images/logo/jpg/bioconductor_logo_rgb.jpg" width="200">
<img alt="Affymetrics" src="http://mms.businesswire.com/media/20150720005017/en/477014/5/2294568_affymetrix_new_logo_no_tagline.jpg" width="200">

RStudio-Microarrays in a Docker Container

What is this?

This project is an example of the use of dockers with the r program lenguage,
the RStudio user interface and the bioconductor packages for affymetrix microarrays.
This microarray pipeline is focused into the fRMA algorithm and the ArrayQualityMetrics
packate for quality.

This project is based on the work of mccahill/rstudio wich also contains knitr and
Rmarkdown libraries to create esasily and nicely formatted output. There is
also just enough of TeX to allow knitr to generate PDF output.

How to pull the container

Pull the container with the command:

[sudo] docker pull fmunoz/rstudio-microarrays

How to run

Run using the default password from the Dockerfile build script:

[sudo] docker run -d -i -t -p 8787:8787 -e USERPASS="badpassword" fmunoz/rstudio-microarrays

Load a volume

[sudo] docker run -d -i -t -p 8787:8787 -e USERPASS="badpassword"  -v /external/directory/for/user:/root/ fmunoz/rstudio-microarrays

How to access

To access the app, point your web browser at
http://localhost:8787/

You will be prompted to login. Use the username 'guest' and the password 'badpassword'

Docker Pull Command
Owner
fmunoz
Source Repository

Comments (1)
fmunoz
10 months ago

There is a problem with plots and arrayQualityMetricsPackage (doesn't run well in rstudio)