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Intervene

An interactive Shiny App for UpSet plots, Venn diagrams and Pairwise heatmaps

Intervene Shiny App provides an interactive interface for intersection and effective visualization of gene or genomic region sets. Currently, Shiny app does not acccept genomic regions as input, but the text files generated by Interve's command line interface can be easily uploaded to further explore and customize the plots in an interactive way. Intervene has three modules:

  • venn to generate Venn diagrams of up-to 6 sets,
  • upset to generate UpSet plots of more than 3 sets and
  • pairwise to compute and visualize pariwise intersections as clustered heatmap.

Install the required packages

Install the following packages:

install.packages(c("shiny","shinydashboard", "devtools", "d3heatmap", "plotly", "gplots", "ggplot2", "gridExtra", "plyr", "UpSetR", "colourpicker", "corrplot", "BBmisc", "readr", "DT"));
source("https://bioconductor.org/biocLite.R"); biocLite(c("RBGL","graph"));
library(devtools); install_github("js229/Vennerable");

Online availability

Intervene Shiny App is freely available at

https://asntech.shinyapps.io/intervene

OR

https://intervene.shinyapps.io/intervene

Support

If you have questions, or found any bug in the program, please write to us at aziz.khan[at]ncmm.uio.no

Cite

If you use Intervene please cite us:

Khan A, Mathelier A. Intervene: a tool for intersection and visualization of multiple gene or genomic region sets. BMC Bioinformatics. 2017;18:287. doi: 10.1186/s12859-017-1708-7