DNAfusion

Identification of gene fusions using paired-end sequencing

Bioconductor version: 3.23 · Package version: 1.14.0

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.

Installation

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

BiocManager::install("DNAfusion")

Details

Maintainer	Christoffer Trier Maansson <ctm@clin.au.dk>
Author	Christoffer Trier Maansson [aut, cre] (ORCID: <https://orcid.org/0000-0002-3071-3437>), Emma Roger Andersen [ctb, rev], Maiken Parm Ulhoi [dtc], Peter Meldgaard [dtc], Boe Sandahl Sorensen [rev, fnd]
License	GPL-3
URL	https://github.com/CTrierMaansson/DNAfusion
Bug Reports	https://github.com/CTrierMaansson/DNAfusion/issues
Downloads rank	243
Source branch	RELEASE_3_23
biocViews	GeneFusionDetection, Genetics, Sequencing, Software, TargetedResequencing

Documentation

DNAfusion \vspace{0.5in}

Download

Source package

Dependencies

Depends: R (>= 4.4.0)

Imports: GenomicRanges, IRanges, Rsamtools, GenomicAlignments, BiocBaseUtils, S4Vectors, GenomicFeatures, TxDb.Hsapiens.UCSC.hg38.knownGene, BiocGenerics

Suggests: knitr, rmarkdown, testthat, sessioninfo, BiocStyle