Package: DNAfusion
Title: Identification of gene fusions using paired-end sequencing
Version: 1.12.0
biocViews: TargetedResequencing, Genetics, GeneFusionDetection,
        Sequencing
Authors@R: 
    c(person(given = "Christoffer Trier", family = "Maansson", , email = "ctm@clin.au.dk", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0002-3071-3437")),
    person(given = "Emma Roger", family = "Andersen", , email = "201907412@post.au.dk", role = c("ctb", "rev")),
    person(given = "Maiken Parm", family = "Ulhoi", , email = "maiken@oncology.au.dk", role = "dtc"),
    person(given = "Peter", family = "Meldgaard", , email = "petemeld@rm.dk", role = "dtc"),
    person(given = "Boe Sandahl", family = "Sorensen", , email = "b.sorensen@clin.au.dk", role = c("rev", "fnd")))
Description: 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.
License: GPL-3
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Suggests: knitr, rmarkdown, testthat, sessioninfo, BiocStyle
VignetteBuilder: knitr
Imports: GenomicRanges, IRanges, Rsamtools, GenomicAlignments,
        BiocBaseUtils, S4Vectors, GenomicFeatures,
        TxDb.Hsapiens.UCSC.hg38.knownGene, BiocGenerics
Depends: R (>= 4.4.0)
BugReports: https://github.com/CTrierMaansson/DNAfusion/issues
URL: https://github.com/CTrierMaansson/DNAfusion
Config/pak/sysreqs: make libbz2-dev liblzma-dev libpng-dev libxml2-dev
        libssl-dev xz-utils zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:19:47 UTC
RemoteUrl: https://github.com/bioc/DNAfusion
RemoteRef: RELEASE_3_22
RemoteSha: 7226d682f1f6f801bed52866bd18c4647d4b0a11
NeedsCompilation: no
Packaged: 2026-01-24 19:57:20 UTC; root
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]
Maintainer: Christoffer Trier Maansson <ctm@clin.au.dk>
Built: R 4.5.2; ; 2026-01-24 20:00:06 UTC; windows
