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DNAfusion

Identification of gene fusions using paired-end sequencing


Bioconductor version: Release (3.18)

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] , 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 "4.3") 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")
Introduction to DNAfusion HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews GeneFusionDetection, Genetics, Sequencing, Software, TargetedResequencing
Version 1.4.0
In Bioconductor since BioC 3.16 (R-4.2) (1.5 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
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Suggests knitr, rmarkdown, testthat, sessioninfo, BiocStyle
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Package Archives

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

Source Package DNAfusion_1.4.0.tar.gz
Windows Binary DNAfusion_1.4.0.zip
macOS Binary (x86_64) DNAfusion_1.4.0.tgz
macOS Binary (arm64) DNAfusion_1.4.0.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