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chimeraviz

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

Visualization tools for gene fusions


Bioconductor version: Development (3.19)

chimeraviz manages data from fusion gene finders and provides useful visualization tools.

Author: Stian Lågstad [aut, cre], Sen Zhao [ctb], Andreas M. Hoff [ctb], Bjarne Johannessen [ctb], Ole Christian Lingjærde [ctb], Rolf Skotheim [ctb]

Maintainer: Stian Lågstad <stianlagstad at gmail.com>

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

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("chimeraviz")

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("chimeraviz")
chimeraviz HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Alignment, Infrastructure, Software
Version 1.29.0
In Bioconductor since BioC 3.5 (R-3.4) (7 years)
License Artistic-2.0
Depends Biostrings, GenomicRanges, IRanges, Gviz, S4Vectors, ensembldb, AnnotationFilter, data.table
Imports methods, grid, Rsamtools, GenomeInfoDb, GenomicAlignments, RColorBrewer, graphics, AnnotationDbi, RCircos, org.Hs.eg.db, org.Mm.eg.db, rmarkdown, graph, Rgraphviz, DT, plyr, dplyr, BiocStyle, checkmate, gtools, magick
System Requirements bowtie, samtools, and egrep are required for some functionalities
URL https://github.com/stianlagstad/chimeraviz
Bug Reports https://github.com/stianlagstad/chimeraviz/issues
See More
Suggests testthat, roxygen2, devtools, knitr, lintr
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package chimeraviz_1.29.0.tar.gz
Windows Binary chimeraviz_1.29.0.zip
macOS Binary (x86_64) chimeraviz_1.29.0.tgz
macOS Binary (arm64) chimeraviz_1.29.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/chimeraviz
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/chimeraviz
Bioc Package Browser https://code.bioconductor.org/browse/chimeraviz/
Package Short Url https://bioconductor.org/packages/chimeraviz/
Package Downloads Report Download Stats