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Protocols

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 citations

 (33)
library_books

Transcriptional profiling of sugarcane leaves and roots under progressive osmotic stress reveals a regulated coordination of gene expression in a spatiotemporal manner

2017
PLoS One
PMCID: 5724895
PMID: 29228055
DOI: 10.1371/journal.pone.0189271

[…] 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; p<0.05) […]

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Genome Guided Phylo Transcriptomic Methods and the Nuclear Phylogentic Tree of the Paniceae Grasses

2017
Sci Rep
PMCID: 5648822
PMID: 29051622
DOI: 10.1038/s41598-017-13236-z
call_split See protocol

[…] . 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 and each of the other […]

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An HDAC3 PROX1 corepressor module acts on HNF4α to control hepatic triglycerides

2017
Nat Commun
PMCID: 5601916
PMID: 28916805
DOI: 10.1038/s41467-017-00772-5
call_split See protocol

[…] eters and 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 was performe […]

library_books

In silico prediction of novel therapeutic targets using gene–disease association data

2017
J Transl Med
PMCID: 5576250
PMID: 28851378
DOI: 10.1186/s12967-017-1285-6

[…] ng 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 at https://gi […]

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Genome Sequence of Pseudomonas stutzeri 273 and Identification of the Exopolysaccharide EPS273 Biosynthesis Locus

2017
Mar Drugs
PMCID: 5532660
PMID: 28698510
DOI: 10.3390/md15070218
call_split See protocol

[…] lopedia of genes and genomes) [], COG (Clusters of Orthologous Groups) [], GO (Gene Ontology) [], NR (Non-Redundant Protein Database databases), and Swiss-Prot []. The Venn diagram was constructed by Vennerable R package []. The CAZy family of glycosyltransferases was determined based on the Carbohydrate-Active enZYmes database []. […]

library_books

Time resolved dual transcriptomics reveal early induced Nicotiana benthamiana root genes and conserved infection promoting Phytophthora palmivora effectors

2017
BMC Biol
PMCID: 5427549
PMID: 28494759
DOI: 10.1186/s12915-017-0379-1

[…] he 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 was est […]


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