Package: topdownr
Title: Investigation of Fragmentation Conditions in Top-Down Proteomics
Version: 1.35.0
Authors@R: c(person("Sebastian", "Gibb", role=c("aut", "cre"),
                    email="mail@sebastiangibb.de",
                    comment=c(ORCID="0000-0001-7406-4443")),
             person("Pavel", "Shliaha", role="aut",
                    email="pavels@bmb.sdu.dk",
                    comment=c(ORCID="0000-0003-3092-0724")),
             person(c("Ole", "Nørregaard"), "Jensen", role="aut",
                    email="jenseno@bmb.sdu.dk",
                    comment=c(ORCID="0000-0003-1862-8528")))
Description: The topdownr package allows automatic and systemic
        investigation of fragment conditions. It creates Thermo
        Orbitrap Fusion Lumos method files to test hundreds of
        fragmentation conditions. Additionally it provides functions to
        analyse and process the generated MS data and determine the
        best conditions to maximise overall fragment coverage.
Depends: R (>= 3.5), methods, BiocGenerics (>= 0.20.0), ProtGenerics
        (>= 1.10.0), Biostrings (>= 2.42.1), S4Vectors (>= 0.12.2)
Imports: grDevices, stats, tools, utils, Biobase, Matrix (>= 1.4-2),
        MSnbase (>= 2.33.5), PSMatch (>= 1.11.4), ggplot2 (>= 2.2.1),
        mzR (>= 2.27.5)
Suggests: topdownrdata (>= 0.2), knitr, rmarkdown, ranger, testthat,
        BiocStyle, xml2
License: GPL (>= 3)
URL: https://codeberg.org/sgibb/topdownr/
BugReports: https://codeberg.org/sgibb/topdownr/issues/
LazyData: true
VignetteBuilder: knitr
Roxygen: list(markdown=TRUE)
RoxygenNote: 7.3.3
biocViews: ImmunoOncology, Infrastructure, Proteomics,
        MassSpectrometry, Coverage
Encoding: UTF-8
Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libuv1-dev
        libxml2-dev libnetcdf-dev libssl-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:46:43 UTC
RemoteUrl: https://github.com/bioc/topdownr
RemoteRef: HEAD
RemoteSha: b3262a2923148d7b3b64672fbfc23f3a8e3e953c
NeedsCompilation: no
Packaged: 2026-05-24 06:33:57 UTC; root
Author: Sebastian Gibb [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-7406-4443>),
  Pavel Shliaha [aut] (ORCID: <https://orcid.org/0000-0003-3092-0724>),
  Ole Nørregaard Jensen [aut] (ORCID:
    <https://orcid.org/0000-0003-1862-8528>)
Maintainer: Sebastian Gibb <mail@sebastiangibb.de>
Built: R 4.6.0; ; 2026-05-24 06:36:47 UTC; unix
