BioVenn protocols

View BioVenn computational protocol

BioVenn statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Venn diagram creation chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

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 in pipelines

 (24)
2018
PMCID: 5838928
PMID: 29527141
DOI: 10.1186/s12014-018-9188-y

[…] there was one peptide containing three “b” and two “z” amino acids, in both cases the values for the acid counterpart (“d”, “e”) were considered for the calculation of the protein properties. biovenn was used for venn diagrams []., we analyzed four single murine kidney tissue slices either with the dtr protocol or with the fasp workflow using 10 and 30 k filter devices. the sample […]

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

[…] grant opp1133649 (pb). tp was funded by a ndm studentship. pb is a jenner institute investigator., 1http://www.cbs.dtu.dk/biotools/seq2logo/index.php (accessed: august 18, 2017)., 2http://www.biovenn.nl/ (accessed: august 16, 2017)., 3http://www.cbs.dtu.dk/services/gibbscluster/ (accessed: august 13, 2017)., 4http://www.iedb.org/ (accessed: august 13, 2017)., […]

2017
PMCID: 5482983
PMID: 28455373
DOI: 10.1242/dev.143479

[…] using the liftover tool of the ucsc genome browser. association of chip-seq peaks with closest genes was analyzed using great software (), and the overlaps of gene sets were analyzed using biovenn (). microrarray data were analyzed using genespring 14.5 software (agilent). the chip-seq data reported in this paper were deposited at gene expression omnibus database with accession number […]

2017
PMCID: 5587817
PMID: 28645154
DOI: 10.1093/nar/gkx536

[…] cutoff of 0.05 (,). categories were collapsed and colored the same in plots if there was >50% overlap of genes within the category containing fewer genes. venn diagrams were generated using biovenn (). reads were plotted in igv 2.3.67 (,). volcano plots were drawn with cummerbund (). mirna target site abundance in differentially regulated genes was assessed using targetscan release 6.2 […]

2017
PMCID: 5686521
PMID: 29152586
DOI: 10.1128/mSystems.00127-17

[…] using psortb analysis, and functional predictions were checked with nemesys (https://www.genoscope.cns.fr/agc/microscope/collabprojects/nemesys.php) (, ). the venn diagram was generated with biovenn ()., the raw fastq files from rna-seq were cleaned for low-quality segments, stretches of n’s, and inclusion of adaptor sequence. overlapping read pairs were collapsed into single reads, […]


To access a full list of citations, you will need to upgrade to our premium service.

BioVenn in publications

 (140)
PMCID: 5946011
PMID: 29780384
DOI: 10.3389/fimmu.2018.00912

[…] (). 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 […]

PMCID: 5908790
PMID: 29674704
DOI: 10.1038/s41389-018-0043-9

[…] full set of gene signatures in the molecular signatures database where gene lists were pre-ranked using -log(fdr)·sign(log2(fold-change)) from the limma analysis. venn diagrams were generated using biovenn (http://www.cmbi.ru.nl/cdd/biovenn /index.php)., microarray datasets have been deposited in geo under the accession number #gse112282., western blot, qrt-pcr, and cell cycle analyses […]

PMCID: 5904183
PMID: 29666442
DOI: 10.1038/s41467-018-03959-6

[…] was applied and go terms with p < 0.05 were included. for visualization of regulated go terms and associated genes the cytoscape software was employed. for visualization of venn diagrams, the biovenn web application was employed., for whole-mount immunostaining, tissues were fixed in 4% paraformaldehyde (pfa) for 2 h at rt or overnight at 4 °c, permeabilised in 0.3% triton-x100 in pbs […]

PMCID: 5893545
PMID: 29636481
DOI: 10.1038/s41467-018-03832-6

[…] samples. genes downregulated by nigt1.2-ox were described in kiba et al. (accession number gse100903 in gene expression omnibus). venn diagrams with numbers of selected genes were generated by biovenn., seedlings were grown in n-free 1/2ms liquid medium supplemented with 1% sucrose at 22 ℃ under continuous light with rotation (120 rpm) for 4 days and treated with 1 mm kcl or 1 mm kno3 […]

PMCID: 5893879
PMID: 29636436
DOI: 10.1128/mBio.00170-18

[…] (log2), and those with only one unique peptide were removed. ratios between conditions were created, and proteins with a fold change of >1.5 were analyzed further. venn diagrams were created in biovenn (), and heat maps were created in perseus., go terms were analyzed with the cluego cytoscape plug-in (version 3.6.0) (, ). the minimum and maximum go levels were set to 3 and 7, respectively. […]


To access a full list of publications, you will need to upgrade to our premium service.

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

BioVenn review

star_border star_border star_border star_border star_border
star star star star star
Anonymous user #1085's avatar image No country

Anonymous user #1085

star_border star_border star_border star_border star_border
star star star star star
Web
Very useful tool!