Manipulation of SQLite-based annotations in Bioconductor

Implements a user-friendly interface for querying SQLite-based annotation data packages.

Hervé Pagès, Marc Carlson, Seth Falcon, Nianhua Li

R (>= 2.7.0), methods, stats4, BiocGenerics (>= 0.29.2),
Biobase (>= 1.17.0), IRanges

DBI, RSQLite, S4Vectors (>= 0.9.25), stats, KEGGREST

utils, hgu95av2.db, GO.db, org.Sc.sgd.db, org.At.tair.db,
RUnit, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db,
reactome.db, AnnotationForge, graph, EnsDb.Hsapiens.v75,
BiocStyle, knitr

00RTobjs.R AllGenerics.R AllClasses.R unlist2.R utils.R SQL.R
FlatBimap.R AnnDbObj-lowAPI.R Bimap.R GOTerms.R
BimapFormatting.R Bimap-envirAPI.R flatten.R
methods-AnnotationDb.R methods-SQLiteConnection.R
methods-geneCentricDbs.R methods-geneCentricDbs-keys.R
methods-ReactomeDb.R methods-OrthologyDb.R loadDb.R
createAnnObjs-utils.R createAnnObjs.NCBIORG_DBs.R
createAnnObjs.NCBICHIP_DBs.R createAnnObjs.ORGANISM_DB.R
createAnnObjs.YEASTCHIP_DB.R createAnnObjs.COELICOLOR_DB.R
createAnnObjs.ARABIDOPSISCHIP_DB.R createAnnObjs.MALARIA_DB.R
createAnnObjs.YEAST_DB.R createAnnObjs.YEASTNCBI_DB.R
createAnnObjs.ARABIDOPSIS_DB.R createAnnObjs.GO_DB.R
createAnnObjs.KEGG_DB.R createAnnObjs.PFAM_DB.R
AnnDbPkg-templates-common.R AnnDbPkg-checker.R
print.probetable.R makeMap.R inpIDMapper.R
test_AnnotationDbi_package.R

c(
    person("Gábor", "Csárdi", , "csardi.gabor@gmail.com", role = c("aut", "cre")),
    person("Kirill", "Müller", role = "aut"),
    person("Jim", "Hester", , "james.f.hester@gmail.com", role = "aut"),
    person("Maëlle", "Salmon", role = "ctb",
           comment = c(ORCID = "0000-0002-2815-0399")),
    person("Posit Software, PBC", role = c("cph", "fnd"))
  )

Tools to read, write, create, and manipulate DESCRIPTION
    files.  It is intended for packages that create or manipulate other
    packages.

callr, covr, gh, spelling, testthat, whoami, withr

'assertions.R' 'authors-at-r.R' 'built.R' 'classes.R'
'collate.R' 'constants.R' 'deps.R' 'desc-package.R'
'description.R' 'encoding.R' 'find-package-root.R' 'latex.R'
'non-oo-api.R' 'package-archives.R' 'read.R' 'remotes.R'
'str.R' 'syntax_checks.R' 'urls.R' 'utils.R' 'validate.R'
'version.R'