Vennerable protocols

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Vennerable specifications

Information


Unique identifier OMICS_19065
Name Vennerable
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 3.1.0.9000
Stability Stable
Requirements
methods
Maintained Yes

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  • person_outline Jonathan Swinton <>

Vennerable in pipelines

 (2)
2017
PMCID: 5427549
PMID: 28494759
DOI: 10.1186/s12915-017-0379-1

[…] log-transformed tpm values and visualised in r with the help of the ’ggplot2’ [] and ’pheatmap’ [] packages. overlap between groups of genes identified in the pca analysis was visualised with the ’vennerable’ package []. differentially expressed genes were identified with the ‘edger’ bioconductor package [] following pairwise comparisons between all the samples. the dispersion parameter […]

2014
PMCID: 4064326
PMID: 24947819
DOI: 10.1038/srep05371

[…] were considered for subsequent analyses. cuffdiff was applied to analyze the differential gene expression between gbm and control. area-proportional venn diagrams were generated using the r package “vennerable” (http://r-forge.r-project.org/projects/vennerable/)., gene ontology analysis was performed using the david functional analysis tool. the bonferroni, benjamini, and fdr (false discovery […]


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Vennerable in publications

 (44)
PMCID: 5724895
PMID: 29228055
DOI: 10.1371/journal.pone.0189271

[…] go and ec terms, and kegg ec biochemical pathways., data analysis and graphics were performed with the r statistical package [] unless stated otherwise. all the graphs were done by ggplot2 [] and vennerable r packages (https://github.com/js229/vennerable). to provide statistical support for physiological and biochemical analyses, we use the tuckey’s hsd (honest significance difference; […]

PMCID: 5648822
PMID: 29051622
DOI: 10.1038/s41598-017-13236-z

[…] and the ya yang pipeline,. as above, raxml, astral, and binning combined with astral were used to infer phylogenies. phylogenetic trees and other figures were generated using figtree, inkscape, and vennerable in r–., for the grass data used for benchmarking, several additional analyses were run. single copy syntenic orthologs were found in a pairwise fashion between o. sativa […]

PMCID: 5607285
PMID: 28931935
DOI: 10.1038/s41598-017-12335-1

[…] between each dataset, human and mouse orthologues were identified using the mouse genome informatics database (http://www.informatics.jax.org). venn diagrams were constructed using the r package vennerable_3.1.0.9000 and genes that existed in all three datasets (primary mouse islet, primary human islet, and mouse islet cell line). we tested the significance of overlap of genes enriched […]

PMCID: 5601916
PMID: 28916805
DOI: 10.1038/s41467-017-00772-5

[…] igg as input. peaks more than threefold over input and >2 rpm in prox1 and >1.5 rpm in hdac3 were used for further downstream analyses. venn diagram was generated using bedtools v2.26.0 and vennerable r package with peaks overlapping at least 50% and having at least 1 rpm in the other chip-seq. motif analyses were performed with homer using 200 bp peak windows. gene ontology […]

PMCID: 5576250
PMID: 28851378
DOI: 10.1186/s12967-017-1285-6

[…] the individual models were rpart [], randomforest [], nnet [], e1071 [] and gbm []. other packages used for data processing and visualisation were biomart [], jsonlite [], ggplot2 [], rtsne [] and vennerable []. release 84 of ensembl [] was used for gene annotation. scibite docstore [] was used for text mining the medline database. all code was versioned using git and is available […]


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