VennMaster protocols

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VennMaster specifications

Information


Unique identifier OMICS_05569
Name VennMaster
Software type Application/Script, Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Version 0.37.3
Stability Stable
Requirements
JRE
Maintained Yes

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Maintainers


  • person_outline Hans Kestler <>
  • person_outline André Müller <>
  • person_outline Johann Kraus <>
  • person_outline Malte Buchholz <>

Publication for VennMaster

VennMaster in pipeline

2012
PMCID: 3280880
PMID: 22249449
DOI: 10.1084/jem.20111980

[…] were used. mutation frequencies were calculated as the number of mutations divided by the number of all nucleotides of the given frame work regions and cdrs. venn diagrams were generated with vennmaster 0.37.4 (2010-04-06). for phylogenetic analysis, sequences were aligned with clustalw 2.0.12 multiple sequence alignment tool (; ). based on the alignment, phylogenetic trees […]


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VennMaster in publications

 (14)
PMCID: 5772169
PMID: 29343442
DOI: 10.1016/j.immuni.2017.12.010

[…] regions (p value ≤ 0.05) were calculated by diffbind v2.0.5 (). intersections, subtractions and merging of the predicted peaks were made with bedtools. proportional venn diagrams were generated with vennmaster (). genome coverage files (bedgraph files) for visualization were generated by makeucscfile.pl (homer) and then converted into tdf files using igvtools with ‘totdf’ option. de novo motif […]

PMCID: 4658477
PMID: 26603754
DOI: 10.1038/srep16923

[…] feasible for more than five sets due to combinatorial explosion in the number of possible set intersections (2n intersections for n sets). although there is a plethora of methods and tools (e.g., vennmaster, venneuler and upset) to either axiomatically or heuristically resolve the issue of optimized visualization of multi-set intersections, a quantitative visualization of many complex […]

PMCID: 4552728
PMID: 26317337
DOI: 10.1371/journal.ppat.1005133

[…] mean values that had significant differences (p≤0.05) between treated and untreated samples were clustered into the 2 groups “up” (upregulated ≥1.00-fold) or “down” (downregulated <1.00-fold). vennmaster (http://sysbio.uni-ulm.de/?software:vennmaster) [] was used to determine the overlap of biochemicals that were either “up” or “down” in any of the treated samples. to visualize the result […]

PMCID: 4415773
PMID: 25928420
DOI: 10.1371/journal.pone.0124504

[…] the top scored overrepresented and overlapping associated networks in the development-associated and microbiota-associated gene sets. these are presented as a euler diagram (generated using vennmaster) in the development associated genes are primarily involved in the diverse biological functions of protein homooligomeration, mitochondria organization and metabolic processes including […]

PMCID: 3601955
PMID: 23527175
DOI: 10.1371/journal.pone.0059369

[…] was determined using the publically available useq package (useq.sourceforge.net). significance parameters were set at an fdr of 10% and two-fold change., venn diagrams were created using the vennmaster program and comparing bcl11b regulated genes to ews/fli repressed genes . gsea was performed by creating a rank ordered list (most up-regulated genes to most repressed genes) using ews/fli […]


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VennMaster institution(s)
Neural Information Processing, University of Ulm, Germany; Internal Medicine I – Gastroenterology, University Hospital Ulm, Germany; Department of Gastroenterology and Endocrinology, University Hospital of Marburg, Germany; Georgetown University, Washington, WA, USA; SRA International, USA; National Institutes of Health, National Cancer Institute, Laboratory of Molecular Pharmacology, Genomics and Bioinformatics Group, USA
VennMaster funding source(s)
Supported by the Intramural Research Program of the NIH, National Cancer Institute, Center for Cancer Research.

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