Vennify

A minimal R Shiny app to generate proportional Venn diagrams from pasted or uploaded gene lists.

Download or clone the repo

• Option 1: Download

  • Click on < > Code ▼ -> Download Zip; unzip the folder to a desired location

• Option 2: Clone using Git

  • In the folder on Rstudio/terminal, run git clone https://github.com/rskanchi/Vennify.git

Running the App

• Require R (>= 4.1.0).
• In R, setwd(<project/folder>) or in RStudio, open the project.
• Install the R packages with install.packages(c("shiny", "eulerr", "gplots", "stringi", "colourpicker")) or restore the project environment if you're using renv.

install.packages("renv")
renv::restore()

• Run the app: In R or Rstudio console, execute shiny::runApp() in the project folder. In RStudio, you can open app.R and click the Run App button in the upper right of the editor.

Input options

Paste lists

• Paste values (one per line) for up to 3 sets.
• Customize each set's label and color.
• Optionally, specify an output folder.

Upload file

• Upload a CSV with set columns (set1, set2, ...) and optional sign columns (sign1, sign2, ...).

• Sign columns could be the log2 fold change, correlation or any other numeric value indicating gene/feature directionality.

• Select which columns to use as set and sign in the same order as set columns.

• Choose custom colors for each set.

  

Output

The output files are saved in the folder path you specify.

• Proportional Venn diagrams (pdf format).
• Unique/overlap set elements and frequencies (csv format).
• If the sign variables are provided, the app will also generate UP and DOWN-regulated venns, lists and frequencies.

Sample output from Upload CSV

Notes

• You can edit the output folder by typing a valid path (local to the machine running the app).
• renv.lock is included for reproducibility; the renv/ folder is excluded to keep the repo light.
• If you want to use renv, install it and uncomment this line in .Rprofile: source("renv/activate.R").

License

This project is licensed under the MIT License.