A rewrite of the graphics layout capabilities, plus some
  support for interaction.

Biobase: Base functions for Bioconductor

R. Gentleman, V. Carey, M. Morgan, S. Falcon

Functions that are needed by many other packages or which
        replace R functions.

tools, tkWidgets, ALL, RUnit, golubEsets

tools.R strings.R environment.R vignettes.R packages.R
AllGenerics.R VersionsClass.R VersionedClasses.R
methods-VersionsNull.R methods-VersionedClass.R DataClasses.R
methods-aggregator.R methods-container.R methods-MIAxE.R
methods-MIAME.R methods-AssayData.R
methods-AnnotatedDataFrame.R methods-eSet.R
methods-ExpressionSet.R methods-MultiSet.R methods-SnpSet.R
methods-NChannelSet.R anyMissing.R rowOp-methods.R
updateObjectTo.R methods-ScalarObject.R zzz.R

Encapsulated Classes with Reference Semantics

person("Winston", "Chang", role = c("aut", "cre"), email = "winston@stdout.org")

Creates classes with reference semantics, similar to R's built-in
    reference classes. Compared to reference classes, R6 classes are simpler
    and lighter-weight, and they are not built on S4 classes so they do not
    require the methods package. These classes allow public and private
    members, and they support inheritance, even when the classes are defined in
    different packages.

knitr, microbenchmark, pryr, testthat, ggplot2, scales

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, utils, stats4, BiocGenerics (>=
0.29.2), Biobase (>= 1.17.0), IRanges

hgu95av2.db, GO.db, org.Sc.sgd.db, org.At.tair.db, KEGG.db,
RUnit, TxDb.Hsapiens.UCSC.hg19.knownGene, hom.Hs.inp.db,
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-Inparanoid.R methods-Inparanoid8.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.INPARANOID_DB.R
createAnnObjs.PFAM_DB.R AnnDbPkg-templates-common.R
AnnDbPkg-checker.R print.probetable.R makeMap.R inpIDMapper.R
test_AnnotationDbi_package.R