gmoviz

DOI: 10.18129/B9.bioc.gmoviz    

Seamless visualization of complex genomic variations in GMOs and edited cell lines

Bioconductor version: Release (3.11)

Genetically modified organisms (GMOs) and cell lines are widely used models in all kinds of biological research. As part of characterising these models, DNA sequencing technology and bioinformatics analyses are used systematically to study their genomes. Therefore, large volumes of data are generated and various algorithms are applied to analyse this data, which introduces a challenge on representing all findings in an informative and concise manner. `gmoviz` provides users with an easy way to visualise and facilitate the explanation of complex genomic editing events on a larger, biologically-relevant scale.

Author: Kathleen Zeglinski [cre, aut], Arthur Hsu [aut], Monther Alhamdoosh [aut] , Constantinos Koutsakis [aut]

Maintainer: Kathleen Zeglinski <kathleen.zeglinski at csl.com.au>

Citation (from within R, enter citation("gmoviz")):

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("gmoviz")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("gmoviz")

 

HTML R Script Advanced usage of gmoviz
HTML R Script Introduction to gmoviz
PDF   Reference Manual
Text   NEWS

Details

biocViews Coverage, GeneticVariability, GenomicVariation, Sequencing, Software, Visualization
Version 1.0.0
In Bioconductor since BioC 3.11 (R-4.0) (< 6 months)
License GPL-3
Depends circlize, GenomicRanges, graphics, R (>= 4.0)
Imports grid, gridBase, Rsamtools, ComplexHeatmap, BiocGenerics, Biostrings, GenomeInfoDb, methods, GenomicAlignments, GenomicFeatures, IRanges, rtracklayer, pracma, colorspace, S4Vectors
LinkingTo
Suggests testthat, knitr, rmarkdown, pasillaBamSubset, BiocStyle, BiocManager
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package gmoviz_1.0.0.tar.gz
Windows Binary gmoviz_1.0.0.zip
macOS 10.13 (High Sierra) gmoviz_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/gmoviz
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/gmoviz
Package Short Url https://bioconductor.org/packages/gmoviz/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.11 Source Archive

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