# Variance-sensitive clustering of omics data Feature-based variance-sensitive clustering of omics data. Optimizes cluster assignment by taking into account individual feature variance. VSClust is available as interactive and user-friendly Shiny webservice and as R package in Bioconductor. For more instructions on both, see below. VSClust was developed at the [Protein Research Group](http://www.sdu.dk/en/Om_SDU/Institutter_centre/Bmb_biokemi_og_molekylaer_biologi/Forskning/Forskningsgrupper/Protein.aspx) Department of Biochemistry and Molecular Biology [University of Southern Denmark](http://www.sdu.dk) ## 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 ## Shiny app ### Web service You can use the implementation on 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. ### Local implementation #### Docker 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 #### Bioconda Install the package in the command-line ``` conda install -c bioconda vsclust run_vsclust_app.sh ``` and access the shiny app through http://localhost:3838 #### Manual installation Install the Bioconductor package `vsclust` In R: ``` if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("vsclust") ``` You can run the shiny app from the server.R or ui.R files in the "inst/shiny" folder using [Rstudio](http://rstudio.com) or run the app on a [shiny-server](https://www.rstudio.com/products/shiny/shiny-server/) Be aware that you need to have all files, the R libraries described in Installation *and* the modified e1071 library installed. ### Build and use Docker image A Dockerfile has been created on top of the rocker/shiny docker image. Copy this repository to a folder and carry out the following command to build the image (takes a while) `docker build -t veitveit/vsclust .` You can also just directly download and run the image by `docker run -t -i -p 3838:3838 veitveit/vsclust` and access the server through http://localhost:3838 ## Command line and R package All operations but the gene set enrichment can be performed via command line running the R script `runVSClust.R` or using the functions of the Bioconductor package `vsclust` ### Installation #### In R: ``` if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("vsclust") ``` ### As conda package TBD ### Usage Please take a look at the vignettes and/or in the help packages of the `vsclust` functions ## Contact For software issues and general questions, please submit an issue. ## License GPL-2 or higher