List of Venn diagram tools for bioinformaticians

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  • The current biomedical hegemony of mass analytical "omics" domains such as genomics, proteomics, and metabolomics has enabled the rapid generation of enormously complex data sets with frequently unwieldy quantities of data points.
  • Venn analysis is frequently used as the initial filtering step for large, complex, and interrelated data corpora.
  • Numerous Venn diagram applications are already accessible for free to aid in the straightforward visual interpretation of biological datasets.
  • The accessible tools for plotting Venn diagrams, on the other hand, are unevenly scattered throughout the literature.
  • Here, we present a guided list to such tools that might assist scientists/researchers/students in visualizing their gene lists and generating biological hypotheses using integrated knowledge from biological pathway and GO databases.

Table 1:List of tools and their features

S. noTool/programNumber of input data sets (maximum)PlatformFunctional informationNumber of citation
1BioVenn3Web-applicationBioVenn outputs lists of identifiers for each of the resulting subsets. If an identifier is recognized as belonging to one of the supported biological databases, the output is linked to that database. Finally, BioVenn can map Affymetrix and EntrezGene identifiers to Ensembl genes.1114
2colorfulVennPlot4RNo-
3DiVenn 2.08Web-applicationshows the gene regulation levels for each gene and integrated KEGG pathway and gene ontology knowledge for the data visualization29
4DrawVenn5RNo
5eulerAPE3SoftwareNo456
6eulerForce5SoftwareNo13
7eulerGlyphs3SoftwareNo160
8GeneSpring-Softwaremicroarray data-
9GeneVenn3Web-applicationGene ontology190
10InteractiVenn6Web-applicationNo1056
11Intervene6Web-applicationupset to generate UpSet plots of multiple sets, and pairwise to compute and visualize intersections of multiple sets as clustered heat maps184
12jvenn6Web-applicationNo761
13Multiple List Comparator6Web-applicationNo-
14NetVenn4Web-applicationThe tool can integrate gene sets with differentially expressed gene on interaction network.29
15nVenn6Web-applicationNo48
16Pangloss Venn diagram generator4Web-applicationNo
17PINA4MS4cytoscape plugginThe Protein Interaction Network Analysis For Multiple Sets (PINA4MS) combines the curated protein-protein interactions from PINA and kinase-substrate relationships from PhosphoSitePlus to identify interactions between and within multiple groups of genes of interest.
18silicocyte-Softwaremicroarray data
19Venn and Euler Diagrams4cytoscape plugginNo
20Venn Diagram Plotter3Web-applicationNo
21VennDiagram4RNo1320
22VennDiagramWeb5Web-applicationNo24
23VennDIS5SoftwareNo33
24Vennerable9RNo-
25VennMaster3Web-applicationGene ontology121
26VennPainter8SoftwareNo62
27VennPlex4SoftwareThis program is able to facilitate the analysis of two to four gene sets and their corresponding expression values in a user-friendly manner97
28VENNTURE6Softwarecellular context with respect to functional GPCR signaling outputs78
29Venny4Web-applicationNo1425

Table 2: List of references and URLs of the above mentioned tools.


S. noTool/programURLReference
1BioVennhttp://www.cmbi.ru.nl/cdd/biovenn/BioVenn – a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams
2colorfulVennPlothttps://cran.r-project.org/web/packages/colorfulVennPlot/index.html-
3DiVenn 2.0https://divenn.tch.harvard.edu/DiVenn: An Interactive and Integrated Web-Based Visualization Tool for Comparing Gene Lists
4DrawVennhttps://rdrr.io/github/barzine/barzinePhdR/man/DrawVenn.html-
5eulerAPEhttps://www.eulerdiagrams.org/eulerAPE/eulerAPE: Drawing Area-Proportional 3-Venn Diagrams Using Ellipses
6eulerForcehttp://www.eulerdiagrams.org/eulerForce/eulerForce: Force-directed layout for Euler diagrams
7eulerGlyphshttp://www.eulerdiagrams.org/eulerGlyphs/Assessing the effect of visualizations on bayesian reasoning through crowdsourcing
9GeneSpringhttp://www.strandgenomics.com/GeneSpring-
10GeneVennhttp://mcbc.usm.edu/genevenn/GeneVenn - A web application for comparing gene lists using Venn diagrams
11InteractiVennwww.interactivenn.net.InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams
12Intervenehttps://asntech.shinyapps.io/intervene.Intervene: a tool for intersection and visualization of multiple gene or genomic region sets
13jvennhttp://jvenn.toulouse.inra.fr/app/index.htmljvenn: an interactive Venn diagram viewer
14Multiple List Comparatorhttps://academic.oup.com/bib/article/22/5/bbab108/6220174?login=true-
15NetVennhttp://probes.pw.usda.gov/NetVenn or http://wheat.pw.usda.gov/NetVenn.NetVenn: an integrated network analysis web platform for gene lists
16nVennhttp://degradome.uniovi.es/cgi-bin/nVenn/nvenn.cgi.nVenn: generalized, quasi-proportional Venn and Euler diagrams
17Pangloss Venn diagram generatorhttp://www.pangloss.com/seidel/Protocols/venn4.cgi-
18PINA4MShttps://apps.cytoscape.org/apps/pina4ms-
19silicocytehttp://www.cytogenomic.com/silicocyte.htm-
20Venn and Euler Diagramshttps://apps.cytoscape.org/apps/vennandeulerdiagrams-
21Venn Diagram Plotterhttp://omics.pnl.gov/software/VennDiagramPlotter.php-
22VennDiagramhttps://cran.r-project.org/web/packages/VennDiagram/index.htmlVennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R
23VennDiagramWebhttp://venndiagram.res.oicr.on.ca/.VennDiagramWeb: a web application for the generation of highly customizable Venn and Euler diagrams
24VennDIShttp://kislingerlab.uhnres.utoronto.ca/projects/VennDIS_v1.0.1.zipVennDIS: A JavaFX-based Venn and Euler diagram software to generate publication quality figures
25Vennerablehttps://github.com/js229/Vennerable#:~:text=Star%2081-,Vennerable%20provides%20Venn%20diagrams%20in%20R.,graphical%20control%20over%20the%20result.-
26VennMasterhttp://www.informatik.uni-ulm.de/ni/mitarbeiter/HKestler/vennhyp/VennMaster: area-proportional Euler diagrams for functional GO analysis of microarrays
27VennPainterhttps://github.com/linguoliang/VennPainter/VennPainter: A Tool for the Comparison and Identification of Candidate Genes Based on Venn Diagrams
28VennPlexhttp://ttc.nci.nih.gov/forms/mta.php.VennPlex--a novel Venn diagram program for comparing and visualizing datasets with differentially regulated datapoints
29VENNTUREhttp://www.nia.nih.govVENNTURE–A Novel Venn Diagram Investigational Tool for Multiple Pharmacological Dataset Analysis
30Vennyhttps://bioinfogp.cnb.csic.es/tools/venny/Oliveros, J.C. (2007-2015) Venny. An Interactive Tool for Comparing Lists with Venn’s Diagrams.


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