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Number of citations per year for the bioinformatics software tool Vennt
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Protocols

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 citations

 (6)
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Virus and dsRNA triggered transcriptional responses reveal key components of honey bee antiviral defense

2017
Sci Rep
PMCID: 5526946
PMID: 28743868
DOI: 10.1038/s41598-017-06623-z
call_split See protocol

[…] ormalization 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. […]

library_books

Transcriptome analysis of creeping bentgrass exposed to drought stress and polyamine treatment

2017
PLoS One
PMCID: 5406032
PMID: 28445484
DOI: 10.1371/journal.pone.0175848

[…] xpression 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 than […]

call_split

A TGFβ PRMT5 MEP50 Axis Regulates Cancer Cell Invasion through Histone H3 and H4 Arginine Methylation Coupled Transcriptional Activation and Repression

2016
Oncogene
PMCID: 5140780
PMID: 27270440
DOI: 10.1038/onc.2016.205
call_split See protocol

[…] 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 with Consensus […]

call_split

RNA seq analysis of virR and revR mutants of Clostridium perfringens

2016
BMC Genomics
PMCID: 4877802
PMID: 27216822
DOI: 10.1186/s12864-016-2706-2
call_split See protocol

[…] 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 gen […]

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Lamin A/C sustains PcG protein architecture, maintaining transcriptional repression at target genes

2015
PMCID: 4639869
PMID: 26553927
DOI: 10.1083/jcb.201504035
call_split See protocol

[…] ere determined to a P value lower than the false discovery rate after Benjamini–Hochberg correction for multiple testing. We used fold changes to filter and select differentially expressed genes with vennt (fold change R1.2). The hypergeometric distribution was computed using R software. GO analysis was performed with DAVID Bioinformatics Resources (). […]

library_books

The role of antigen presenting cells in the induction of HIV 1 latency in resting CD4+ T cells

2015
Retrovirology
PMCID: 4567795
PMID: 26362311
DOI: 10.1186/s12977-015-0204-2

[…] (Additional file : Table S3). Differential expression was calculated using Voom/Limma [] and visualization performed using Degust [] (http://victorian-bioinformatics-consortium.github.io/degust/) and Vennt [] (http://drpowell.github.io/vennt/). Genes with fewer than 10 reads across every sample were removed from the analysis.APC subsets were categorized as latency-inducing and latency-non-inducing […]


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