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gmoviz

This is the development version of gmoviz; for the stable release version, see gmoviz.

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


Bioconductor version: Development (3.19)

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 "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews Coverage, GeneticVariability, GenomicVariation, Sequencing, Software, Visualization
Version 1.15.0
In Bioconductor since BioC 3.11 (R-4.0) (4 years)
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
System Requirements
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Suggests testthat, knitr, rmarkdown, pasillaBamSubset, BiocStyle, BiocManager
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Package Archives

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

Source Package gmoviz_1.15.0.tar.gz
Windows Binary gmoviz_1.15.0.zip (64-bit only)
macOS Binary (x86_64) gmoviz_1.15.0.tgz
macOS Binary (arm64) gmoviz_1.15.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/gmoviz
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/gmoviz
Bioc Package Browser https://code.bioconductor.org/browse/gmoviz/
Package Short Url https://bioconductor.org/packages/gmoviz/
Package Downloads Report Download Stats