DNAfusion
This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see DNAfusion.
Identification of gene fusions using paired-end sequencing
Bioconductor version: 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("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 | ||
| 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 |
See More
| Suggests | knitr, rmarkdown, testthat, sessioninfo, BiocStyle |
| 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 | 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 [email protected]:packages/DNAfusion |
| Bioc Package Browser | https://code.bioconductor.org/browse/DNAfusion/ |
| Package Short Url | https://bioconductor.org/packages/DNAfusion/ |
| Package Downloads Report | Download Stats |