VennDiagram protocols

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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

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Versioning


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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

 (12)
2018
PMCID: 5940145
PMID: 29535148
DOI: 10.1534/g3.118.200174

[…] 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 […]

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

[…] (microsoft, redmond, wa, usa) and used for subsequent analysis., nucleotide fasta files for candidate transcripts were generated using the ‘seqinr’ package (), venn diagrams were drawn with the ‘venndiagram’ package (), using r version 3.3.2 (). distribution of gene ontology (go) terms within the sequences that were differentially expressed at all time point (2,798 deg) were determined using […]

2017
PMCID: 5405463
PMID: 28446171
DOI: 10.1186/s12864-017-3705-7

[…] analysis (pca) was used to summarise the distribution of gene expression values of the samples using functions in the r base package and venn diagrams were generated for the data using the r package venndiagram []., in order to generate functional terms associated with the genes of interest, the software blast2go [] was used to annotate the ibeetle t. castaneum genome annotation []. the r […]

2017
PMCID: 5431893
PMID: 28500316
DOI: 10.1038/s41598-017-01856-4

[…] and lusc samples and the different status of methylation loci correlated with rna expression between control and cancer in luad or lusc samples. the r packages (http://www.r-project.org/), such as venndiagram and ggplot2 were utilized for other statistical analyses and data visualization. by using multiple bioinformatics tools based on different databases, we were able to identify […]

2017
PMCID: 5717538
PMID: 29249983
DOI: 10.3389/fphys.2017.00980

[…] was identified using gene ontology's -biological process category available via cluego-a cystoscape plugin (bindea et al., ) and david v6.8 (dennis et al., ). venn diagram was created using the “venndiagram” package available through r/bioconductor (chen and boutros, )., we utilized the drug gene interaction database (dgidb) (wagner et al., ) to identify a list of expert-curated […]


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VennDiagram in publications

 (62)
PMCID: 5929573
PMID: 29672509
DOI: 10.1371/journal.pgen.1007357

[…] 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 […]

PMCID: 5861657
PMID: 29558886
DOI: 10.1186/s12864-018-4596-y

[…] and expression levels from rsem software. genes with fdr < 0.05 and |log2fold change| (|log2fc|) ≥ 1 were assigned as differentially expressed genes (degs). venn diagram was created using venndiagram [] to show the quantitative distribution of degs in different comparisons. gene ontology (go) annotation was performed using blast2go software [] to classify the degs. pathway analysis […]

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

[…] 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 […]

PMCID: 5820949
PMID: 29229736
DOI: 10.1128/IAI.00490-17

[…] was performed with panther () using the s. typhimurium go annotation, while kegg pathway analysis was performed with the gage r package (r 3.3.1) (), using the s. typhi (stt) kegg annotation. the venndiagram () and gplots r packages were used for data visualization., for rt-qpcr, 2 μg of rna was treated with dnase (promega) prior to reverse transcription with moloney murine leukemia virus […]

PMCID: 5785829
PMID: 29416569
DOI: 10.1186/s13100-018-0109-4

[…] method and euclidean distance measure) to generate a sidelong dendrogram. the r environment was also used for representation of tfs and cag gene co-occurrence in relevant h. pylori genomes using the venndiagram package []., fisher’s exact test was used for statistical analysis of contingency tables using graphpad prism 7.01 (graphpad software, california, usa)., additional file 1: additional […]


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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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