jvenn protocols

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jvenn specifications

Information


Unique identifier OMICS_05562
Name jvenn
Interface Web user interface
Restrictions to use None
Input data Lists
Output data Venn diagram, lists
Output format PNG, SVG, CSV
Programming languages Javascript
License GNU General Public License version 3.0, GNU General Public License version 2.0
Computer skills Basic
Version 1.8
Stability Stable
Requirements
jQuery, jvenn.min.js
Maintained Yes

Maintainer


  • person_outline Jérôme Mariette <>

Publication for jvenn

jvenn in pipelines

 (7)
2018
PMCID: 5913888
PMID: 29685100
DOI: 10.1186/s12864-018-4680-3

[…] protein clustering of predicted protein sequences was conducted with orthofinder version 1.1.4 [] at an expected value 0.001. a venn diagram of protein orthologous groups was constructed with jvenn []., gene functional annotation (e.g. go and interpro terms) and enrichment was found for orthologous groups using stringdb [] and david bioinformatics resource [, , ]., genome data for bfp […]

2017
PMCID: 5525251
PMID: 28738780
DOI: 10.1186/s12864-017-3945-6

[…] 0.8 and relative change ≥ 2”. to identify the pathways that deus participate in, kegg enrichment analysis was performed by phyper. heatmap was generated using mev and venn diagram was created using jvenn []., additional file 1: figure s1. additional file 2: table s1. additional file 3: table s2. additional file 4: figure s2. additional file 5: table s3. additional file 6: figure s3. additional […]

2017
PMCID: 5567372
PMID: 28831170
DOI: 10.1038/s41598-017-08690-8

[…] as differentially expressed. the fpkm value was used to assess the expression levels of unigenes. the venn diagram of degs was generated using an online software (http://bioinfo.genotoul.fr/jvenn/). the heatmap was generated with z-score normalized fpkm values using the online tools available at omicshare (http://www.omicshare.com/). the clustering analysis was performed based […]

2017
PMCID: 5609589
PMID: 28971068
DOI: 10.3389/fcimb.2017.00383

[…] et al., ), kegg automatic annotation system (moriya et al., ), cazy database (lombard et al., ), smart database (letunic et al., ), and cat server (park et al., ). venn diagrams were designed in jvenn server (bardou et al., ). assessment for presence of virulence factors, antibiotic resistance genes, and toxins was done by executing local blast to compare all the orfs predicted […]

2017
PMCID: 5729405
PMID: 29237423
DOI: 10.1186/s12864-017-4354-6

[…] associations as edges. the r package rcirco [] was used to illustrate master regulators, which we defined as snps that had associations with multiple genes. to generate venn diagrams, we used jvenn, a plug-in for the jquery javascript library []. boxplots were produced with the r package ggplot. the r package pcit [] was used to analyze the correlation between the expression variation […]

jvenn in publications

 (39)
PMCID: 5913888
PMID: 29685100
DOI: 10.1186/s12864-018-4680-3

[…] protein clustering of predicted protein sequences was conducted with orthofinder version 1.1.4 [] at an expected value 0.001. a venn diagram of protein orthologous groups was constructed with jvenn []., gene functional annotation (e.g. go and interpro terms) and enrichment was found for orthologous groups using stringdb [] and david bioinformatics resource [, , ]., genome data for bfp […]

PMCID: 5903623
PMID: 29664968
DOI: 10.1371/journal.pone.0195967

[…] of < 0.05% were removed. alpha diversity of level 0.05 was performed on the otus and chao 1 and simpson indices were obtained using the ram package [] in r. venn diagram was constructed by jvenn tool []. non-parametric analyses, including analysis of similarities (anosim), permutation multivariate analysis of variance (permanova) and canonical analysis of principal (cap) coordinates […]

PMCID: 5853956
PMID: 29503181
DOI: 10.1016/j.chom.2018.01.008

[…] (369 genes) and p. yoelii (907 genes) were individually transformed into orthologs of the five other plasmodium species. ortholog sets (syntenic/non-syntenic) among the species were identified using jvenn () and assigned according to the species identifier pf, pv, pk, pb, pc or py ( and )., to investigate the association between heterochromatic region and distribution of kir and sicavar genes […]

PMCID: 5859471
PMID: 29559843
DOI: 10.7150/ijbs.22868

[…] orthologous groups (kog) and cazy , for analyzing the results obtained. the differentially expressed gene lists of the respective experimental conditions were compared using venny 2.1 and jvenn softwares. we have retrieved sample level fpkm (fragments per kilobase of transcripts per million) values, p-values and log fold change values from supplementary files provided for gse84529 […]

PMCID: 5760519
PMID: 29317671
DOI: 10.1038/s41598-017-18447-y

[…] r package mixomics. the otu networks were generated by qiime pipeline and networks were visualized using cytoscape 3.4.0 by applying the spring embedded layout. venn diagrams were generated using jvenn (available at http://bioinfo.genotoul.fr/jvenn) ., all prevailing local, national and international regulations and conventions, and normal scientific ethical practices, have been respected. […]

jvenn institution(s)
Plate-forme bio-informatique Genotoul/MIA-T, INRA, Borde Rouge, Castanet-Tolosan, France; Plate-forme SIGENAE/GenPhySE, INRA, Borde Rouge, Castanet-Tolosan, France

jvenn review

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Anonymous user #440

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Web
Great tool.
Very useful to generate venn up to 6 classes and really easy to integrable within our web site !