Package: Spectra
Title: Spectra Infrastructure for Mass Spectrometry Data
Version: 1.22.0
Description: The Spectra package defines an efficient infrastructure
        for storing and handling mass spectrometry spectra and
        functionality to subset, process, visualize and compare spectra
        data. It provides different implementations (backends) to store
        mass spectrometry data. These comprise backends tuned for fast
        data access and processing and backends for very large data
        sets ensuring a small memory footprint.
Authors@R: c(person(given = "RforMassSpectrometry Package Maintainer",
                    email = "maintainer@rformassspectrometry.org",
                    role = "cre"),
             person(given = "Laurent", family = "Gatto",
                    email = "laurent.gatto@uclouvain.be",
                    role = "aut",
                    comment = c(ORCID = "0000-0002-1520-2268")),
             person(given = "Johannes", family = "Rainer",
                    email = "Johannes.Rainer@eurac.edu",
                    role = "aut",
                    comment = c(ORCID = "0000-0002-6977-7147")),
             person(given = "Sebastian", family = "Gibb",
                    email = "mail@sebastiangibb.de",
                    role = "aut",
                    comment = c(ORCID = "0000-0001-7406-4443")),
             person(given = "Philippine", family = "Louail",
                    email = "philippine.louail@eurac.edu",
                    role = c("aut"),
                    comment = c(ORCID = "0009-0007-5429-6846")),
             person(given = "Jan", family = "Stanstrup",
                    email = "stanstrup@gmail.com",
                    role = "ctb",
                    comment = c(ORCID = "0000-0003-0541-7369")),
             person(given = "Nir", family = "Shahaf",
                    email = "gabbianon@gmail.com",
                    role = "ctb"),
             person(given = "Mar", family = "Garcia-Aloy",
                    email = "mar.garcia@fmach.it",
                    comment = c(ORCID = "0000-0002-1330-6610"),
                    role = "ctb"),
            person(given = "Guillaume", family = "Deflandre",
                    email = "guillaume.deflandre@uclouvain.be",
                    comment = c(ORCID = "0009-0008-1257-2416"),
                    role = "ctb"),
            person(given = "Ahlam", family = "Mentag",
                    email = "ahlammentag8@gmail.com",
                    comment = c(ORCID = "0009-0008-5438-7067"),
                    role = "ctb"))
Depends: R (>= 4.1.0), S4Vectors, BiocParallel
Imports: ProtGenerics (>= 1.39.2), methods, IRanges, MsCoreUtils (>=
        1.23.6), graphics, grDevices, stats, tools, utils, fs,
        BiocGenerics, MetaboCoreUtils, data.table
Suggests: testthat, knitr (>= 1.1.0), MsDataHub, roxygen2, BiocStyle
        (>= 2.5.19), mzR (>= 2.19.6), rhdf5 (>= 2.32.0), rmarkdown,
        vdiffr (>= 1.0.0), msentropy, patrick
License: Artistic-2.0
LazyData: false
VignetteBuilder: knitr
BugReports: https://github.com/RforMassSpectrometry/Spectra/issues
URL: https://github.com/RforMassSpectrometry/Spectra
biocViews: Infrastructure, Proteomics, MassSpectrometry, Metabolomics
Encoding: UTF-8
RoxygenNote: 7.3.3
Roxygen: list(markdown=TRUE)
Collate: 'hidden_aliases.R' 'AllGenerics.R' 'MsBackend-functions.R'
        'MsBackend.R' 'MsBackendCached.R'
        'MsBackendDataFrame-functions.R' 'MsBackendDataFrame.R'
        'MsBackendHdf5Peaks-functions.R' 'MsBackendHdf5Peaks.R'
        'MsBackendMemory-functions.R' 'MsBackendMemory.R'
        'MsBackendMzR-functions.R' 'MsBackendMzR.R'
        'Spectra-estimatePrecursorMz.R' 'Spectra-functions.R'
        'Spectra.R' 'Spectra-neutralLoss.R' 'Spectra-precursorPurity.R'
        'countIdentifications.R' 'fft_spectrum.R' 'functions-util.R'
        'mz-delta-functions.R' 'peak-list-functions.R'
        'peaks-functions.R' 'plotting-functions.R' 'zzz.R'
Config/pak/sysreqs: cmake make libuv1-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2026-04-28 12:53:31 UTC
RemoteUrl: https://github.com/bioc/Spectra
RemoteRef: RELEASE_3_23
RemoteSha: eb19bc2dc13e75db61534d1c7a293286d3010d0a
NeedsCompilation: no
Packaged: 2026-04-29 14:05:30 UTC; root
Author: RforMassSpectrometry Package Maintainer [cre],
  Laurent Gatto [aut] (ORCID: <https://orcid.org/0000-0002-1520-2268>),
  Johannes Rainer [aut] (ORCID: <https://orcid.org/0000-0002-6977-7147>),
  Sebastian Gibb [aut] (ORCID: <https://orcid.org/0000-0001-7406-4443>),
  Philippine Louail [aut] (ORCID:
    <https://orcid.org/0009-0007-5429-6846>),
  Jan Stanstrup [ctb] (ORCID: <https://orcid.org/0000-0003-0541-7369>),
  Nir Shahaf [ctb],
  Mar Garcia-Aloy [ctb] (ORCID: <https://orcid.org/0000-0002-1330-6610>),
  Guillaume Deflandre [ctb] (ORCID:
    <https://orcid.org/0009-0008-1257-2416>),
  Ahlam Mentag [ctb] (ORCID: <https://orcid.org/0009-0008-5438-7067>)
Maintainer: RforMassSpectrometry Package Maintainer <maintainer@rformassspectrometry.org>
Built: R 4.6.0; ; 2026-04-29 14:11:43 UTC; windows
