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

S4 generic functions needed by many Bioconductor packages.

Biobase, IRanges, GenomicRanges, AnnotationDbi, oligoClasses,
oligo, affyPLM, flowClust, affy, RUnit, DESeq2

S3-classes-as-S4-classes.R append.R as.data.frame.R
as.vector.R cbind.R dge.R plotMA.R duplicated.R eval.R
Extremes.R funprog.R get.R is.unsorted.R lapply.R mapply.R
match.R nrow.R order.R paste.R rank.R rep.R row_colnames.R
sets.R sort.R table.R tapply.R unique.R unlist.R boxplot.R
image.R density.R residuals.R weights.R xtabs.R clusterApply.R
annotation.R combine.R normalize.R normarg-utils.R show-utils.R
strand.R updateObject.R update.R testPackage.R
test_BiocGenerics_package.R zzz.R

c(person("Emmanuel", "Paradis", role = c("aut", "cre", "cph"), email = "Emmanuel.Paradis@ird.fr"),
  person("Simon", "Blomberg", role = c("aut", "cph")),
  person("Ben", "Bolker", role = c("aut", "cph")),
  person("Julien", "Claude", role = c("aut", "cph")),
  person("Hoa Sien", "Cuong", role = c("aut", "cph")),
  person("Richard", "Desper", role = c("aut", "cph")),
  person("Gilles", "Didier", role = c("aut", "cph")),
  person("Benoit", "Durand", role = c("aut", "cph")),
  person("Julien", "Dutheil", role = c("aut", "cph")),
  person("Olivier", "Gascuel", role = c("aut", "cph")),
  person("Christoph", "Heibl", role = c("aut", "cph")),
  person("Daniel", "Lawson", role = c("aut", "cph")),
  person("Vincent", "Lefort", role = c("aut", "cph")),
  person("Pierre", "Legendre", role = c("aut", "cph")),
  person("Jim", "Lemon", role = c("aut", "cph")),
  person("Rosemary", "McCloskey", role = c("aut", "cph")),
  person("Johan", "Nylander", role = c("aut", "cph")),
  person("Rainer", "Opgen-Rhein", role = c("aut", "cph")),
  person("Andrei-Alin", "Popescu", role = c("aut", "cph")),
  person("Manuela", "Royer-Carenzi", role = c("aut", "cph")),
  person("Klaus", "Schliep", role = c("aut", "cph")),
  person("Korbinian", "Strimmer", role = c("aut", "cph")),
  person("Damien", "de Vienne", role = c("aut", "cph")))