DESCRIPTION

Package: CompoundDb
Type: Package
Title: Creating and Using (Chemical) Compound Annotation Databases
Version: 1.11.2
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'