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Welcome to the repository of VSClust developed at the

Protein Research Group
Department of Biochemistry and Molecular Biology
University of Southern Denmark

Citation

When using VSClust, please cite our paper:
Veit Schwämmle, Ole N Jensen; VSClust: Feature-based variance-sensitive clustering of omics data, Bioinformatics, , bty224, https://doi.org/10.1093/bioinformatics/bty224

We provide a shiny app for interactive analysis, a command-line version for running VSClust as script in R and a docker version of the tool to avoid installation issues.

Shiny app

Web service

You can use our web server http://computproteomics.bmb.sdu.dk:

http://computproteomics.bmb.sdu.dk/Apps/VSClust

Be aware that the tool does allow only one user to run the background R calculations at a time. Therefore the app might become temporarily irresponsive. However, multiple sessions are separated and your data won't be shared between sessions or overwritten.

Implementation on own computer

The easiest option is to use the docker image:

docker pull veitveit/vsclust

docker run -t -i -p 3838:3838 veitveit/vsclust

and access the server through http://localhost:3838/VSClust/

You can run the shiny app from the server.R or ui.R files using Rstudio or run the app on a shiny-server

Be aware that you need to have all files, the R libraries described in Installation and the modified e1071 library installed.

Installation

Install the following R libraries: Mfuzz, matrixStats, limma, qvalue, shiny, clusterProfiler, RDAVIDWebService, parallel, shinyjs and shinythemes. In R: source("https://bioconductor.org/biocLite.R")
biocLite(c("Mfuzz", "matrixStats", "limma", "qvalue", "shiny", "clusterProfiler", "RDAVIDWebService", "parallel", "shinyjs", "shinythemes"))

Download the files into a folder and install the library e1071FuzzVec. You might need to compile the library on your computer:
Run R CMD INSTALL e1071FuzzVec_Installation from the command line. You need to be in the VSClust folder. For Windows users, replace R by InstallationPath/R.exe.

Build and use Docker image

A Dockerfile has been created on the basis of an OpenSuse distribution. Copy the repository to a folder and carry out the following command to build the images (takes a while)

docker build -t veitveit/vsclust .

You can run the image by

docker run -t -i -p 3838:3838 veitveit/vsclust

and access the server through http://localhost:3838/VSClust/

Command line

All operations but the gene set enrichment can be performed via command line running the R script runVSClust.R

Usage

Given that you installed the e1071FuzzVec library, open the R script and change the relevant file names and parameters. The different operations are described in the R file.

Installation

The e1071FuzzVec library needs to be compiled and installed, see above.

Contact

For software issues and general questions, please submit an issue.

License

GPL-2 or higher