Package: CompoundDb
Type: Package
Title: Creating and Using (Chemical) Compound Annotation Databases
Version: 1.12.1
Authors@R: c(person(given = "Jan", family = "Stanstrup",
                    email = "stanstrup@gmail.com",
		    role = c("aut"),
		    comment = c(ORCID = "0000-0003-0541-7369")),
             person(given = "Johannes", family = "Rainer",
	            email = "johannes.rainer@eurac.edu",
		    role = c("aut", "cre"),
		    comment = c(ORCID = "0000-0002-6977-7147")),
             person(given = "Josep M.", family = "Badia",
		    email = "josepmaria.badia@urv.cat",
		    role = c("ctb"),
		    comment = c(ORCID = "0000-0002-5704-1124")),
             person(given = "Roger", family = "Gine",
		    email = "alrgibe9@gmail.com",
		    role = c("aut"),
		    comment = c(ORCID = "0000-0003-0288-9619")),
             person(given = "Andrea", family = "Vicini",
	            email = "andrea.vicini@eurac.edu",
		    role = c("aut"),
		    comment = c(ORCID = "0000-0001-9438-6909")),
            person(given = "Prateek", family = "Arora",
	            email = "prateek.arora@unibe.ch",
		    role = c("ctb"),
		    comment = c(ORCID = "0000-0003-0822-9240"))
		    )
Description: CompoundDb provides functionality to create and use (chemical)
    compound annotation databases from a variety of different sources such as
    LipidMaps, HMDB, ChEBI or MassBank. The database format allows to store in
    addition MS/MS spectra along with compound information. The package provides
    also a backend for Bioconductor's Spectra package and allows thus to match
    experimetal MS/MS spectra against MS/MS spectra in the database. Databases
    can be stored in SQLite format and are thus portable.
Depends: R (>= 4.1), methods, AnnotationFilter, S4Vectors
Imports: BiocGenerics, ChemmineR, tibble, jsonlite, dplyr, DBI, dbplyr,
        RSQLite, Biobase, ProtGenerics (>= 1.35.3), xml2, IRanges,
        Spectra (>= 1.15.10), MsCoreUtils, MetaboCoreUtils,
        BiocParallel, stringi
Suggests: knitr, rmarkdown, testthat, BiocStyle (>= 2.5.19),
        MsBackendMgf
URL: https://github.com/RforMassSpectrometry/CompoundDb
BugReports: https://github.com/RforMassSpectrometry/CompoundDb/issues
biocViews: MassSpectrometry, Metabolomics, Annotation
VignetteBuilder: knitr
License: Artistic-2.0
RoxygenNote: 7.3.2
Roxygen: list(markdown=TRUE)
Encoding: UTF-8
Collate: 'AllGenerics.R' 'AnnotationFilters.R' 'createCompDbPackage.R'
        'CompDb.R' 'CompDb-methods.R' 'IonDb.R' 'IonDb-methods.R'
        'MsBackendCompDb-functions.R' 'MsBackendCompDb.R'
        'query-engine.R' 'spectrum-import-functions.R'
        'utility-functions.R'
git_url: https://git.bioconductor.org/packages/CompoundDb
git_branch: RELEASE_3_21
git_last_commit: 7fffee6
git_last_commit_date: 2025-05-19
Repository: Bioconductor 3.21
Date/Publication: 2025-05-22
NeedsCompilation: no
Packaged: 2025-05-22 22:29:01 UTC; biocbuild
Author: Jan Stanstrup [aut] (ORCID: <https://orcid.org/0000-0003-0541-7369>),
  Johannes Rainer [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-6977-7147>),
  Josep M. Badia [ctb] (ORCID: <https://orcid.org/0000-0002-5704-1124>),
  Roger Gine [aut] (ORCID: <https://orcid.org/0000-0003-0288-9619>),
  Andrea Vicini [aut] (ORCID: <https://orcid.org/0000-0001-9438-6909>),
  Prateek Arora [ctb] (ORCID: <https://orcid.org/0000-0003-0822-9240>)
Maintainer: Johannes Rainer <johannes.rainer@eurac.edu>
Built: R 4.5.0; ; 2025-05-23 13:30:26 UTC; windows
