DNAfusion

DOI: 10.18129/B9.bioc.DNAfusion  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see DNAfusion.

Identification of gene fusions using paired-end sequencing

Bioconductor version: 3.16

Paired-end sequencing of cfDNA generated BAM files can be used as input to discover EML4-ALK variants. 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] , 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>

Installation

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

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

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")

 

HTML	R Script	Introduction to DNAfusion
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneFusionDetection, Genetics, Sequencing, Software, TargetedResequencing
Version	1.0.0
In Bioconductor since	BioC 3.16 (R-4.2) (< 6 months)
License	GPL-3
Depends	R (>= 4.2.0)
Imports	bamsignals, GenomicRanges, IRanges, Rsamtools, GenomicAlignments, BiocBaseUtils, S4Vectors
LinkingTo
Suggests	knitr, rmarkdown, testthat, sessioninfo, BiocStyle
SystemRequirements
Enhances
URL	https://github.com/CTrierMaansson/DNAfusion
BugReports	https://github.com/CTrierMaansson/DNAfusion/issues
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	DNAfusion_1.0.0.tar.gz
Windows Binary	DNAfusion_1.0.0.zip
macOS Binary (x86_64)	DNAfusion_1.0.0.tgz
macOS Binary (arm64)	DNAfusion_1.0.0.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