GenVisR protocols

GenVisR statistics

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Tool usage distribution map

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Associated diseases

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GenVisR specifications

Information


Unique identifier OMICS_11309
Name GenVisR
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.0.4
Stability Stable
Requirements
AnnotationDbi, stats, grid, BiocGenerics, IRanges, GenomicRanges, Rsamtools, utils, testthat, Biostrings, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, biomaRt, GenomicFeatures, scales, gtools, knitr, reshape2, DBI, TxDb.Hsapiens.UCSC.hg19.knownGene, R(>=3.3.0), plyr(>=1.8.3), gridExtra, ggplot2(>=0.9.2), gtable, roxygen2, RMySQL, viridis, FField
Maintained Yes

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Maintainer


  • person_outline Zachary Skidmore <>

Publication for GenVisR

GenVisR in pipelines

 (2)
2018
PMCID: 5839398
PMID: 29515767
DOI: 10.18632/oncotarget.24188

[…] pathogenic variants detected in the tumor were selected to orientate the patients to her2 inhibitors. we have mapped the mutations on a schematic structure of the her2 membranous receptor using the genvisr package []., patients harboring a druggable molecular alteration were prospectively oriented and treated in either a phase 1 or an off label use of molecular targeted agent, based […]

2017
PMCID: 5643378
PMID: 29038591
DOI: 10.1038/s41598-017-13650-3

[…] a specified region for each sample, and coverage space indicates the total exon region for each cancer type. the mutational landscape and transition-transversion plot were visualized with r package “genvisr”. differentially mutated sites of amino acid alterations and differentially mutated protein domains were plotted using mutationmapper (http://www.cbioportal.org/mutation_mapper.jsp) […]


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GenVisR in publications

 (5)
PMCID: 5793777
PMID: 29092957
DOI: 10.1101/mcs.a002329

[…] with activation scores of >3 or <−3 were selected. molecular targets of drugs mentioned in this study were retrieved from ., loh events and cnas were illustrated using the bioconductor package genvisr (). heatmaps were generated using the bioconductor package complexheatmap () and r package gplots., dna and rna sequencing data have been deposited in the european genome-phenome archive […]

PMCID: 5839398
PMID: 29515767
DOI: 10.18632/oncotarget.24188

[…] pathogenic variants detected in the tumor were selected to orientate the patients to her2 inhibitors. we have mapped the mutations on a schematic structure of the her2 membranous receptor using the genvisr package []., patients harboring a druggable molecular alteration were prospectively oriented and treated in either a phase 1 or an off label use of molecular targeted agent, based […]

PMCID: 5790521
PMID: 29423104
DOI: 10.18632/oncotarget.23664

[…] read coverage distribution differences between tumor and matched normal using methods previously published []. mutation locations were mapped to a protein framework using the lolliplot function in genvisr package (http://bioconductor.org/package/genvisr) implemented in r3.3.0., reverse phase protein array (rppa) data was generated by the cancer genome atlas (tcga) research network []. […]

PMCID: 5643378
PMID: 29038591
DOI: 10.1038/s41598-017-13650-3

[…] a specified region for each sample, and coverage space indicates the total exon region for each cancer type. the mutational landscape and transition-transversion plot were visualized with r package “genvisr”. differentially mutated sites of amino acid alterations and differentially mutated protein domains were plotted using mutationmapper (http://www.cbioportal.org/mutation_mapper.jsp) […]

PMCID: 5436135
PMID: 28489074
DOI: 10.1038/ncomms15165

[…] calculations were done using r. the r packages, dendextend, gplots and corrplot were used to plot coloured dendrograms, heatmaps and correlation/similarity matrices, and the bioconductor package genvisr was used to plot mutation waterfall plots., the number of pubmed central articles mentioning one of the ccle kidney cancer cell lines was determined with the pubmed central search builder […]


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GenVisR institution(s)
McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA; Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
GenVisR funding source(s)
The National Human Genome Research Institute (K99HG007940); the National Cancer Institute (K22CA188163)

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