DNAfusion

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

Identification of gene fusions using paired-end sequencing

Bioconductor version: Development (3.21)

DNAfusion can identify gene fusions such as EML4-ALK based on paired-end sequencing results. This package was developed using position deduplicated BAM files generated with the AVENIO Oncology Analysis Software. These files are made using the AVENIO ctDNA surveillance kit and Illumina Nextseq 500 sequencing. This is a targeted hybridization NGS approach and includes ALK-specific but not EML4-specific probes.

Author: Christoffer Trier Maansson [aut, cre] (ORCID: ), Emma Roger Andersen [ctb, rev], Maiken Parm Ulhoi [dtc], Peter Meldgaard [dtc], Boe Sandahl Sorensen [rev, fnd]

Maintainer: Christoffer Trier Maansson <ctm at clin.au.dk>

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

Installation

To install this package, start R (version "4.5") and enter:


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

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

BiocManager::install("DNAfusion")

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("DNAfusion")

Introduction to DNAfusion	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GeneFusionDetection, Genetics, Sequencing, Software, TargetedResequencing
Version	1.9.0
In Bioconductor since	BioC 3.16 (R-4.2) (2 years)
License	GPL-3
Depends	R (>= 4.2.0)
Imports	bamsignals, GenomicRanges, IRanges, Rsamtools, GenomicAlignments, BiocBaseUtils, S4Vectors, GenomicFeatures, TxDb.Hsapiens.UCSC.hg38.knownGene, BiocGenerics
System Requirements
URL	https://github.com/CTrierMaansson/DNAfusion
Bug Reports	https://github.com/CTrierMaansson/DNAfusion/issues

Suggests	knitr, rmarkdown, testthat, sessioninfo, BiocStyle
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
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Build Report	Build Report

Package Archives

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

Source Package	DNAfusion_1.9.0.tar.gz
Windows Binary (x86_64)	DNAfusion_1.9.0.zip
macOS Binary (x86_64)	DNAfusion_1.9.0.tgz
macOS Binary (arm64)	DNAfusion_1.9.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/DNAfusion
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/DNAfusion
Bioc Package Browser	https://code.bioconductor.org/browse/DNAfusion/
Package Short Url	https://bioconductor.org/packages/DNAfusion/
Package Downloads Report	Download Stats