Venn diagram generation software tools | High-throughput sequencing data analysis
Venn diagrams are commonly used to display list comparison. In biology, they are widely used to show the differences between gene lists originating from different differential analyses, for instance. They thus allow the comparison between different experimental conditions or between different methods.
Enables to investigate set-based data. UpSet is a visualization technique for the quantitative analysis of sets, their intersections, and aggregates of intersections. User can visualize set intersections in a matrix layout and introduces aggregates based on groupings and queries. An open source R package which allows data exploration and generation of set visualizations is also available.
Allows users to compare and visualize biological lists using Venn diagrams. BioVenn is a web application that generates circular area-proportional Venn diagrams from lists of biological identifiers. The software supports a wide range of identifiers from the most used biological databases (Affymetrix, COG, Ensembl, EntrezGene, Gene Ontology, InterPro, IPI, KEGG Pathway, KOG, PhyloPat [and RefSeq).
Produces highly customizable, publication quality Venn and Euler figures with a simple and intuitive graphical user interface (GUI). VennDIS is a platform-independent open source software written in Java. It supports several types of data input, such as simple lists, excel style tables, and pre-calculated values for overlaps and differences. Based on the user input, it analyzes the data and instantaneously offers the user suitable diagram options.
Assists users in comparing lists. Venny provides an interactive application with Venn's diagrams, a figure that shows all possible logical relations between a finite collection of different sets. It permits to compare 2, 3 or 4 lists of data. It also offers an offline version that consists on a single standard html file. Finally, this method allows basic customization of user’s diagrams (line weight, font size and style).
Allows users to build and analyze Venn diagrams. InteractiVenn is a web-based tool that provides the ability to interactively visualize the effect of successive unions of up to six sets. The unions may be guided either by a binary tree or by a list. The software enables the analysis of combinations of sets of elements in part or in total, affording additional observations on the interactions between joined sets.
Identifies and defines microbes via reads analysis. MICRA employs read mapping methods to make use of the increasing number of sequenced microbial genomes. The working consists in four parts: (1) pre-processing, (2) sequence identification, (3) identification of the closest reference genome and plasmids by the core part and (4) the post-analysis. This pipeline software is available as a download version and as a web interface.
A web platform for comparison and annotation of orthologous gene clusters among multiple species. OrthoVenn provides comprehensive coverage of vertebrates, metazoa, protists, fungi, plants and bacteria for identify orthologous gene clusters and supports user define species to upload customized protein sequences. It has an efficient and interactive graphic tool which provide a Venn diagram view for comparing two to six species protein sequences. The only thing user need to do is choosing species or upload protein sequences.
With this tool you can calculate the intersection(s) of list of elements. It will generate a textual output indicating which elements are in each intersection or are unique to a certain list. If the number of lists is lower than 6 it will also produce a graphical output in the form of a venn diagram. You have the choice between symmetric (default) or non symmetric venn diagrams. Currently you are able to calculate the intersections of at maximum 30 lists. The graphical output is produced in SVG and PNG format.
Allows generation of highly customizable, high-resolution Venn diagrams with up to four sets and Euler diagrams of two or three sets. VennDiagram allows drawing Euler diagrams using circles and/or ellipses with two or three sets and generation of high resolution TIFF files that are standard in publications. The software can assist the promotion of the usage of automatically generated Venn diagrams within computational pipelines.
Allows simultaneous analysis of multiple large and complex pharmacological datasets. VENNTURE provides an interface for Edwards Venn diagram generation. The software facilitates the analysis of two to six sets of any length of dataset. It can be useful in the analysis of complex datasets in pharmacology, genomics, and bioinformatics research fields. Applied to complex sets of signaling data, VENNTURE can assist in the elucidation of the subtle effects that environmental perturbations can exert upon dose-dependent ligand actions.
Generates Euler and Venn diagrams. nVenn is built on a simulation algorithm to create figures with an arbitrary number of sets. It creates n-dimensional Venn diagrams and rearranges with a self-correcting simulation the inserted circles of given areas in each region. This software is available as a graphical and command line interface and as a web-based application with additional tools for the analysis of the diagrams.
Permits researchers to conduct investigation and construct high-quality publication-ready figures. canvasDesigner can be used to arrange any number of different types of plots in SVG format that can be exported by canvasXpress or other visualization tools. It provides functionalities to adjust plot in size and position freely on the canvas. This tool allows users to modify the font size of: sample label, y-axis label, plot decoration or sample title.
Simultaneously compares up to three multifarious datasets by aggregating and propagating information from the bottom to the top level and produces a graphical output in Cytoscape. The underlying concept of CoVennTree is to bring information from the leaf level up to the root node while maintaining the properties of the content of every dataset. With the introduction of weighted Venn structures, the amounts and relationships of data associated with different conditions can be correlated and simultaneously aggregated without losing relevant information. CoVennTree has been integrated into the Galaxy ToolShed and can be directly downloaded and integrated into the user instance.
Draws area-proportional 3-Venn diagrams using ellipses. eulerAPE is an automated method that generates an exact diagram for most of the cases, and when it fails, the best diagram obtained through the hill climbing search is displayed, together with the inaccuracy values for each region. This method is based on the simple hill climbing optimization technique to draw an area-proportional diagram with ellipses in a time that is relatively fast and that maintains users’ attention.
Provides a birds-eye view of the evolutionary relatedness of whole-transcriptomes. VennBLAST is an integrated software that combines a fast-parallelized BLAST filtering utility with whole-transcriptomic alignment comparison. It depicts the results in an intuitive Venn diagram, illustrating simple set relationships between numbers of BLAST comparisons. It also enables the dissection of genes into meaningful subgroups which can then be further analyzed using various tools.
Provides a statistical basis for estimating area-proportional circular Venn and Euler diagrams on real data. Venneuler is an algorithm that produces (i) a circular Venn diagram when the data can be fit by a circular Venn diagram, (ii) an area-proportional circular Venn diagram when the data can be fit by an area proportional circular Venn diagram, (iii) an area-proportional circular Euler diagram when data can be fit by that model, and (iv) a statistically-justifiable approximation to an area proportional circular Venn or Euler diagram when the data can be fit approximately by one of these models.
Provides an alternative visualization approach with area-proportional Euler diagrams. VennMaster was integrated into the GoMiner software. That integration provides a seamless interface for user, and eliminates the overhead of performing file operations and managing external files. This application is implemented as a platform-independent open source Java application. It shows set relationships with semi-quantitative size information in a single diagram to support biological hypothesis formulation.
Combines cross-platform gene expression data using a fast interval-matching algorithm. AnyExpress is a toolkit that can combine cross-platform gene expression data, process data from both open- and closed-platforms, select a custom target reference, filter out undesirable probes or reads based on custom-defined biological features, and perform quantile-normalization with a large number of microarray samples.
Creates Venn diagrams from two or three gene lists. GeneVenn is a web application that generates Venn diagrams with hyperlinks, on each area on the diagram, showing the related gene list. Each gene name has linked to the related information in NCBI’s Entrez Nucleotide database. Users can modify every element of the generated diagram, including font, color and title.