BioVenn statistics

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Protocols

BioVenn specifications

Information


Unique identifier OMICS_05567
Name BioVenn
Interface Web user interface
Restrictions to use None
Input data Some lists of identifiers.
Output data A Venn diagram.
Output format SVG,PNG
Computer skills Basic
Stability Stable
Maintained Yes

Maintainers


  • person_outline Tim Hulsen
  • person_outline Jacob de Vlieg
  • person_outline Wynand Alkema

Publication for BioVenn

BioVenn citations

 (89)
library_books

Discrimination Between Human Leukocyte Antigen Class I Bound and Co Purified HIV Derived Peptides in Immunopeptidomics Workflows

2018
Front Immunol
PMCID: 5946011
PMID: 29780384
DOI: 10.3389/fimmu.2018.00912

[…] k/services/) (). Sequence logos of identified peptides were produced using the default settings for Shannon type logos in Seq2logo2.0 (). Area-proportional Venn diagrams were created using the online BioVenn tool (). Gibbs Clustering analysis was performed with the online GibbsCluster2.0 server using the default settings for MHC class I ligands with 1–5 clusters (). For comparison to mass spectrom […]

library_books

MYR1 Dependent Effectors Are the Major Drivers of a Host Cell’s Early Response to Toxoplasma, Including Counteracting MYR1 Independent Effects

2018
MBio
PMCID: 5885026
PMID: 29615509
DOI: 10.1128/mBio.02401-17

[…] with average RPKM ratios of ≥1.5 were counted as changed in expression.Heat maps were generated using Gene E (https://software.broadinstitute.org/GENE-E/index.html). Venn diagrams were created using BioVenn (). […]

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Activation of DAF 16/FOXO by reactive oxygen species contributes to longevity in long lived mitochondrial mutants in Caenorhabditis elegans

2018
PLoS Genet
PMCID: 5862515
PMID: 29522556
DOI: 10.1371/journal.pgen.1007268
call_split See protocol

[…] n R v. 3.4.1. Gene names, gene IDs, and predicted function annotations were downloaded using the biomaRt package v. 2.34.0.Venn diagrams of overlapping genes were generated using the free online tool BioVenn: http://www.biovenn.nl/. Heat maps were generated using the free online tool from the Broad Institute Morpheus: (https://software.broadinstitute.org/morpheus/). […]

library_books

First insight into the viral community of the cnidarian model metaorganism Aiptasia using RNA Seq data

2018
PeerJ
PMCID: 5835348
PMID: 29507840
DOI: 10.7717/peerj.4449

[…] 100% of all aposymbiotic, partially populated, and fully symbiotic Aiptasia samples were considered to be core virome members. The different viromes, including the core virome, were visualized using BioVenn (). […]

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Carbon Dioxide Mediates the Response to Temperature and Water Activity Levels in Aspergillus flavus during Infection of Maize Kernels

2017
Toxins
PMCID: 5793092
PMID: 29271897
DOI: 10.3390/toxins10010005
call_split See protocol

[…] d an average read count of less than 10 across all samples were removed prior to WGNCA analysis. Principle Component Analysis plots and heat maps were generated using R. Venn Diagrams were created by BioVenn []. Gene ontology term enrichment analysis for WGCNA clusters was conducted using Fungifun2 []. Rendering of Gene Networks was performed using Cytoscape v3.4.0 []. KEGG annotation was produced […]

call_split

The microbiomes of blowflies and houseflies as bacterial transmission reservoirs

2017
Sci Rep
PMCID: 5701178
PMID: 29176730
DOI: 10.1038/s41598-017-16353-x
call_split See protocol

[…] NCBI taxonomy to generate a table with MEGAN 5. PERMANOVA and ANOVA statistical analysis were performed with phyloseq., as implemented in the tool MicrobiomeAnalyst. Venn diagrams were generated with BioVenn using the ‘species’ level table as an input to generate area-proportional representation.The alignment of assigned reads against full reference genomes of the M. domestica Salivary Gland Hyper […]

Citations

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BioVenn institution(s)
Computational Drug Discovery, CMBI, NCMLS, Radboud University Nijmegen Medical Centre, HB Nijmegen, Netherlands

BioVenn review

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Anonymous user #1085

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Web
Very useful tool!