S4 generic functions needed by many Bioconductor packages.

methods, utils, graphics, stats, parallel

Biobase, S4Vectors, IRanges, GenomicRanges, Rsamtools,
AnnotationDbi, oligoClasses, oligo, affyPLM, flowClust, affy,
DESeq2, MSnbase, annotate, RUnit

S3-classes-as-S4-classes.R utils.R normarg-utils.R
hotfix73465.R replaceSlots.R append.R as.data.frame.R as.list.R
as.vector.R cbind.R do.call.R duplicated.R eval.R Extremes.R
funprog.R get.R grep.R is.unsorted.R lapply.R lengths.R
mapply.R match.R matrix-summary.R mean.R nrow.R order.R paste.R
rank.R rep.R row_colnames.R sets.R sort.R start.R subset.R t.R
table.R tapply.R unique.R unlist.R unsplit.R relist.R var.R
which.R boxplot.R image.R density.R IQR.R mad.R residuals.R
weights.R xtabs.R clusterApply.R annotation.R combine.R
dbconn.R dge.R fileName.R normalize.R Ontology.R
organism_species.R path.R plotMA.R plotPCA.R score.R strand.R
updateObject.R testPackage.R zzz.R

A powerful and elegant high-level data visualization
  system inspired by Trellis graphics, with an emphasis on
  multivariate data. Lattice is sufficient for typical graphics needs,
  and is also flexible enough to handle most nonstandard requirements.
  See ?Lattice for an introduction.

Dirk Eddelbuettel <edd@debian.org> with contributions 
 by Antoine Lucas, Jarek Tuszynski, Henrik Bengtsson, Simon Urbanek,
 Mario Frasca, Bryan Lewis, Murray Stokely, Hannes Muehleisen,
 Duncan Murdoch, Jim Hester, Wush Wu, Qiang Kou, Thierry Onkelinx, 
 Michel Lang, Viliam Simko and Kurt Hornik.

Create Compact Hash Digests of R Objects

Implementation of a function 'digest()' for the creation 
 of hash digests of arbitrary R objects (using the 'md5', 'sha-1', 'sha-256', 
 'crc32', 'xxhash' and 'murmurhash' algorithms) permitting easy comparison of R
 language objects, as well as a function 'hmac()' to create hash-based
 message authentication code. Please note that this package is not meant to
 be deployed for cryptographic purposes for which more comprehensive (and
 widely tested) libraries such as 'OpenSSL' should be used.