grecolab/eutopia repository overview

A solUTion for Omics data PreprocessIng and Analysis

Graphically accessible guided workflow for preprocessing and analysis of omics data. Supports Agilent 2-color, Agilent 1-color, Affymetrix, and Illumina methylation microarray platforms (Ongoing efforts to add support for RNA-Seq data). Discreetly separated steps in analysis designed in R Shiny, incorporates widely used microarray analysis practices and R packages. Reporting is and data interpretation is leveraged from dynamically generated plots.

The source code is available at the GitHub repository https://github.com/Greco-Lab/eUTOPIA⁠.

⁠Install Docker application for Windows 10 Home

https://docs.docker.com/toolbox/toolbox_install_windows/⁠

⁠Install Docker application for Windows 10 64bit: Pro, Enterprise or Education

https://docs.docker.com/docker-for-windows/install/⁠

⁠Install Docker application for Mac

https://docs.docker.com/docker-for-mac/install/⁠

⁠Pull the eUTOPIA docker image:

docker pull grecolab/eutopia

⁠Run the eUTOPIA docker image, map http port 3838 on the host port 8787:

docker run --rm -p 8787:3838 grecolab/eutopia

⁠Using eUTOPIA:

Open your browser and visit (if you choose to map to other port replace 8787 in the url with the correct one): http://localhost:8787/eUTOPIA⁠

⁠Issues with running eUTOPIA docker image and access via url

⁠1) Docker toolbox

• Window 10 Home versions and Older versions of Windows might require some BIOS configuration to enable virtualization technology.
• I suggest using the Kitematic (alpha) for maintaining the docker image and identifying the correct url. The host and port might change based on the virtual machine.
• Use the Oracle VM VirtualBox for specifying the desired RAM (Base Memory) and Processors.

⁠Reference Paper:

Marwah, V. S., Scala, G., Kinaret, P. A. S., Serra, A., Alenius, H., Fortino, V., & Greco, D. (2019). eUTOPIA: solUTion for Omics data PreprocessIng and Analysis. Source code for biology and medicine, 14(1), 1. More information at: https://link.springer.com/article/10.1186/s13029-019-0071-7⁠

⁠Data for demo:

Sample data can be found at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE92900⁠

The raw data can be downloaded from: ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE92nnn/GSE92900/suppl/GSE92900_raw_data_files.tar.gz ** note: this file has to be decompressed

The pheno data matrix can be found at: https://github.com/Greco-Lab/eUTOPIA/blob/master/sample_data/Phenotype_File.tsv⁠

The platform annotation file can be found at: https://github.com/Greco-Lab/eUTOPIA/blob/master/sample_data/GeneList%5C028005_D_GeneList_20190110.txt⁠