[This article was first published on R – Myscape, and kindly contributed to R-bloggers]. (You can report issue about the content on this page here)Want to share your content on R-bloggers? click here if you have a blog, or here if you don't.OverviewIn general, set operations are very useful for comparing lists of things. These lists can contain any strings, such as gene or species names. Set operations are also a good way to identify unique or shared genes across sets of analysis results. The freeCount SO app will help you perform set operations with gene lists, which can be produced from differential expression or network analysis.Potential QuestionsWhat shared genes are driving the patterns of DE in all genotypes?What genes are driving the patterns of DE across treatments?Which DE genes share patterns of co-expression in a given network module?Learning GoalsLearn how to perform set operations with ggVennDiagramPractice comparing lists of gene namesUnderstand how to identify shared and unique genesRelatedThis tutorial is the fifth in a series on omics data analysis:Differential Expression Analysis with freeCountFunctional Analysis with freeCountNetwork Analysis with freeCountFunctional Analysis of Networks with freeCountggVennDiagramThe ggVennDiagram R package enables fancy Venn plots with 2-7 sets and generates publication quality figures. It also support upset plots with unlimited number of sets from version 1.4.4.Before StartingThe exercise in this tutorial will be using the freeCount apps in RStudio on a personal computer. Make sure that you have the following tools downloaded, installed, and up-to-date on your personal computer:R software environmentRStudio desktop applicationFor Windows users, additionally install RTools.It is also possible to run the freeCount apps online through Posit Cloud. To see how, checkout the freeCount Bioinformatics Analysis Apps on Posit Cloud tutorial.Input DataDownload the tribolium gene list 1 fileDownload the tribolium gene list 2 fileDownload the tribolium gene list 3 fileDownload the tribolium gene list 4 fileTip! After clicking the above linked data, right click and select Save As… to download the above files in the necessary formats.The Analysis AppThe following steps show you how to get and start running the freeCount set operations (SO) app.Download the freeCount R Shiny applicationsGo to https://github.com/ElizabethBrooks/freeCountClick the green < > Code buttonClick Download ZIPExtract the freeCount-main directory Navigate to the apps directoryOpen the SO.R file in RStudioClick Install on the yellow banner to install the necessary R packages (or run the code on lines 10 to 15)Click the Run App button in the upper right corner of the source paneAnalysis ProcessPerform the following steps to make aUpload the four data setsDownload the two-way venn diagram resultsDowload the three-way venn diagram resultsDownload the four-way venn diagram results1. Upload DataUpload the data sets (lists) that you want to compare.Input DataFirst, upload a file with the list of things that you want to compare. These lists can contain can be any strings, such as gene or species names. In this tutorial we are using the tribolium gene list 1 file.Next, upload the second file with a list. In this tutorial we are using the tribolium gene list 2 file. After upload the second file, analysis results will begin to appear. You can also continue to upload sets/lists that you want to compare (up to 4 sets).Third, upload the third file with a list. In this tutorial we are using the tribolium gene list 3 file.Finally, upload the fourth file with a list. In this tutorial we are using the tribolium gene list 4 file. Up to 4 sets can be compared with the freeCount SO app.Note that the gene names in these files are actually IDs that are specific to the species and database.2. Download Two-Way VennDownload the two-way venn diagram results from the Venn Diagrams tab.Under each venn diagram are drop down lists and download buttons, which allow you to export specific set intersections. This will allow you to select unique or shared gene lists across the sets that you are comparing.3. Download Three-Way VennDownload the three-way venn diagram results from the Venn Diagrams tab.4. Download Four-Way VennDownload the four-way venn diagram results from the Venn Diagrams tab.To leave a comment for the author, please follow the link and comment on their blog: R – Myscape.R-bloggers.com offers daily e-mail updates about R news and tutorials about learning R and many other topics. Click here if you're looking to post or find an R/data-science job.Want to share your content on R-bloggers? click here if you have a blog, or here if you don't.Continue reading: Set Operations with freeCount