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

S original by Steve Dutky <sdutky@terpalum.umd.edu> initial R
        port and extensions by Martin Maechler; revised and modified
        by Steve Dutky

Functions for bitwise operations on integer vectors.

CGHbase: Base functions and classes for arrayCGH data analysis.

R (>= 2.10), methods, Biobase (>= 2.5.5), marray

Contains functions and classes that are needed by arrayCGH packages.

allGeneric.R classes.R private.R tools.R methods-cghRaw.R
methods-cghSeg.R methods-cghCall.R methods-cghRegions.R

Calling aberrations for array CGH tumor profiles.

R (>= 2.0.0), impute(>= 1.8.0), DNAcopy (>= 1.6.0), methods,
Biobase, CGHbase (>= 1.15.1), snowfall

Calls aberrations for array CGH data using a six state mixture model as well as several biological concepts that are ignored by existing algorithms. Visualization of profiles is also provided.