VennDiagram statistics

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Citations per year

Number of citations per year for the bioinformatics software tool VennDiagram
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Tool usage distribution map

This map represents all the scientific publications referring to VennDiagram per scientific context
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Associated diseases

This word cloud represents VennDiagram usage per disease context
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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
testthat, R(≥2.14.1), grid(≥2.14.1), futile.logger
Maintained Yes

Download


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Versioning


No version available

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 citations

 (83)
library_books

Robustness encoded across essential and accessory replicons of the ecologically versatile bacterium Sinorhizobium meliloti

2018
PLoS Genet
PMCID: 5929573
PMID: 29672509
DOI: 10.1371/journal.pgen.1007357

[…] egrative Genomics Viewer v2.3.97 []. Scatter plots, functional enrichment plots, box plots, and line plots were generated in R using the ggplot2 package []. Venn diagrams were produced in R using the VennDiagram package []. The genome map was prepared using the circos v0.67–7 software []; the sliding window insertion density was calculated with the geom_histogram function of ggplot2, and the GC sk […]

library_books

A comparative genomics study of carbohydrate/glucose metabolic genes: from fish to mammals

2018
BMC Genomics
PMCID: 5896114
PMID: 29642853
DOI: 10.1186/s12864-018-4647-4

[…] rthologues across these species; then, we merged each organism’s KEGG gene lists with orthologues from the other four species. The overlapping genes in the five data sets were manually removed by the VennDiagram [] package of R program; this process was performed online using the VENNY program (http://bioinformatics.psb.ugent.be/webtools/Venn/). Finally, we constructed five vertebrate carbohydrate […]

library_books

In vitro gentamicin exposure alters caveolae protein profile in cochlear spiral ligament pericytes

2018
Proteome Sci
PMCID: 5938607
PMID: 29760588
DOI: 10.1186/s12953-018-0132-x

[…] etected in at least two of the three mass spectrometry runs were considered for further bioinformatic analysis. The latter was performed with R version 3.3.1 (R Core Team) and visualization done with VennDiagram R package [] (https://www.r-project.org). […]

library_books

Genomic insights into the broad antifungal activity, plant probiotic properties, and their regulation, in Pseudomonas donghuensis strain SVBP6

2018
PLoS One
PMCID: 5851621
PMID: 29538430
DOI: 10.1371/journal.pone.0194088

[…] a phylogenetic tree was built by means of FastTree 2.1, as aforementioned. The whole approach is described as a workflow in . A Venn diagram was constructed with R software v. 3.4.0 [], employing the VennDiagram package and all the ORFs (PEGs) found in every P. donghuensis genome as database. […]

library_books

Identification of General Patterns of Sex Biased Expression in Daphnia, a Genus with Environmental Sex Determination

2018
PMCID: 5940145
PMID: 29535148
DOI: 10.1534/g3.118.200174

[…] o-one orthologs in all three species. We then compared this list with our list of sex-DE genes (adjusted p < 0.05), as well as the lists of sex-DE genes in D. galeata and D. pulex (; ). The R package VennDiagram () was used for visualization of sex-DE genes in the three species.We then focused on the core subset of 675 orthologous genes that were found to be consistently sex-DE in all three specie […]

library_books

STAT3 precedes HIF1α transcriptional responses to oxygen and oxygen and glucose deprivation in human brain pericytes

2018
PLoS One
PMCID: 5843348
PMID: 29518129
DOI: 10.1371/journal.pone.0194146

[…] expression of genes of a fold change (fc) >1.5 of the Illumina data set and BRGs were extracted for each transcription factor. The JNSH fc>1.5 lists were used to construct Venn diagrams in R with the VennDiagram-package []. The BRGs of STAT3 and HIF1α were imported into the Python software and analysed with the default settings except that all GO:terms used in the analysis were from: GO database v […]


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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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