gmoviz

DOI: 10.18129/B9.bioc.gmoviz    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see gmoviz.

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

Bioconductor version: 3.15

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>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("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	1.8.0
In Bioconductor since	BioC 3.11 (R-4.0) (2.5 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
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_1.8.0.tar.gz
Windows Binary	gmoviz_1.8.0.zip
macOS Binary (x86_64)	gmoviz_1.8.0.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