DESCRIPTION

Package: topdownr
Title: Investigation of Fragmentation Conditions in Top-Down Proteomics
Version: 1.25.1
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 (>= 2.3.10),
    PSMatch (>= 1.6.0),
    ggplot2 (>= 2.2.1),
    mzR (>= 2.27.5)
Suggests:
    topdownrdata (>= 0.2),
    knitr,
    rmarkdown,
    ranger,
    testthat,
    BiocStyle,
    xml2
License: GPL (>= 3)
URL: https://github.com/sgibb/topdownr/
BugReports: https://github.com/sgibb/topdownr/issues/
LazyData: true
VignetteBuilder: knitr
Roxygen: list(markdown=TRUE)
RoxygenNote: 7.3.0
biocViews: ImmunoOncology, Infrastructure, Proteomics, MassSpectrometry, Coverage
Encoding: UTF-8