Vennt specifications

Information


Unique identifier OMICS_26084
Name Vennt
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 0.8.4
Stability Stable
Maintained Yes

Additional information


http://www.vicbioinformatics.com/software.vennt.shtml

Information


Unique identifier OMICS_26084
Name Vennt
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Additional information


http://www.vicbioinformatics.com/software.vennt.shtml

Vennt in publications

 (7)
PMCID: 5526946
PMID: 28743868
DOI: 10.1038/s41598-017-06623-z

[…] method and the default pooled dispersion model (benjamini-hochberg correction; significantly differentially expressed genes (degs) had q-value ≤ 0.05). venn diagrams were generated using vennt. to further investigate the function of the degs, representative protein sequences (the longest sequence if there were splice variants) of every known honey bee gene were blasted against the d. […]

PMCID: 5460342
PMID: 28634572
DOI: 10.3389/fcimb.2017.00219

[…] translocation assays; dr. c. lo, for imaging expertise; dr. a. mcalister, for advice on the expression of his-tagged proteins; danqing yin (hudson institute of medical research), for performing the vennt analysis; dr. a. grubman, for assistance with construction of the cloning vectors; and s. panckridge (hudson institute of medical research) and c. ferrero for graphics expertise., funding. […]

PMCID: 5406032
PMID: 28445484
DOI: 10.1371/journal.pone.0175848

[…] level of de genes across treatments, each pair of de genes was analyzed in turn (wc vs ws, dc vs ds, wc vs dc, ws vs dc, and ws vs ds) using edger (version 2.14) []. a web-based tool called vennt (version 0.8.1) [] was utilized for examining lists of de genes that are either up- or down-regulated defined at a false discovery rate threshold (fdr) of 0.001 and log2 fold change larger […]

PMCID: 5140780
PMID: 27270440
DOI: 10.1038/onc.2016.205

[…] for each replicate were determined with htseq-count, and differential expression between replicates was measured using deseq2 and edger within the chipster package . overlaps were determined using vennt (http://drpowell.github.io/vennt/). fpkm (fragments per kilobase per million reads) were computed with cufflinks 2.2.1. enriched functional annotations among genes were determined […]

PMCID: 4877802
PMID: 27216822
DOI: 10.1186/s12864-016-2706-2

[…] over-represented categories in the gene lists could be identified. finally, to determine genes that were regulated by both virr and revr, the differentially expressed gene lists were analyzed in the vennt program (http://www.vicbioinformatics.com/software.vennt.shtml). vennt generates dynamic venn diagrams from differential expressed gene lists, which enables the identification of overlapping […]


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