VennDiagram protocols

VennDiagram specifications

Information


Unique identifier OMICS_05570
Name VennDiagram
Alternative name VennDiagramWeb
Software type Package/Module
Interface Command line interface
Restrictions to use None
Output format TIFF
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.6.20
Stability Stable
Requirements grid, futile.logger
Maintained Yes

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Documentation


Maintainer


  • person_outline Paul Boutros <>

Additional information


A web interface is available at: http://venndiagram.res.oicr.on.ca/

Information


Unique identifier OMICS_05570
Name VennDiagram
Alternative name VennDiagramWeb
Interface Web user interface
Restrictions to use None
Input data DNA sequences.
Input format CSV,TSV,TXT
Output data Venn and Euler diagrams
Output format TIFF,PNG,SVG
Programming languages R
License GNU General Public License version 2.0
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Paul Boutros <>

Additional information


A web interface is available at: http://venndiagram.res.oicr.on.ca/

Publications for VennDiagram

VennDiagram IN pipelines

 (9)
2017
PMCID: 5307927
PMID: 28196480
DOI: 10.1186/s12711-017-0295-4

[…] regions that were significantly associated with the target traits were inferred by simwalk2.9 [22], and linkage disequilibrium blocks were defined using default parameters of haploview4.2 [23]. the venndiagram in r package was used to draw a venn diagram that showed the loci that were in common among the four populations and the four methods., the descriptive statistics for the nine growth […]

2017
PMCID: 5328969
PMID: 28293249
DOI: 10.3389/fpls.2017.00271

[…] wa, usa) and used for subsequent analysis., nucleotide fasta files for candidate transcripts were generated using the ‘seqinr’ package2 (charif and lobry, 2007), venn diagrams were drawn with the ‘venndiagram’ package3 (chen and boutros, 2011), using r version 3.3.24 (r core team, 2014). distribution of gene ontology (go) terms within the sequences that were differentially expressed […]

2017
PMCID: 5537386
PMID: 28795085
DOI: 10.1016/j.dib.2017.07.018

[…] were considered and are provided as supplementary material 1 in csv file format with log2-intensity averages for experimental groups and fold changes. we used the r function from the package venndiagram [8], to visualize how differential gene expression profiles through each experimental factor overlap (fig. 2). we implemented a heatmap for these genes (fig. 3) and subsets of top 10 up- […]

2016
PMCID: 4964045
PMID: 27464550
DOI: 10.1186/s12864-016-2923-8

[…] annotation, the number of gene models identified by each assembly method using the 180 m dataset from the two reference protein sets was visualized as quadruple venn diagrams, constructed by the venndiagram package in the r software environment (www.r-project.org). genome-guided assembly using the ae. aegypti reference genome was not included in this analysis because of the above-mentioned […]

2016
PMCID: 4999207
PMID: 27560151
DOI: 10.1371/journal.pone.0161667

[…] a pipeline [16]. we used the benjamini-hochberg method to calculate false discovery rate (fdr, fdr < 0.05) for multiple testing [34]. visualization of data was accomplished using the r packages venndiagram (http://cran.r-project.org/web/packages/venndiagram/index.html), pheatmap (https://cran.r-project.org/web/packages/pheatmap/index.html), and ggplot2 (www.ggplo2.org)., to validate […]

VennDiagram institution(s)
Informatics and Biocomputing Platform, Ontario Institute for Cancer Research, MaRS Centre, South Tower, Toronto, ON, Canada
VennDiagram funding source(s)
Supported by the Ontario Institute for Cancer Research through funding provided by the Government of Ontario, and grant number MOP57903 from the Canadian Institutes of Health Research.

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