Utility function for defining S3 methods

Methods that simplify the setup of S3 generic functions and S3 methods.  Major effort has been made in making definition of methods as simple as possible with a minimum of maintenance for package developers.  For example, generic functions are created automatically, if missing, and naming conflict are automatically solved, if possible.  The method setMethodS3() is a good start for those who in the future may want to migrate to S4.  This is a cross-platform package implemented in pure R that generates standard S3 methods.

R object-oriented programming with or without references

Methods and classes for object-oriented programming in R with or without references.  Large effort has been made on making definition of methods as simple as possible with a minimum of maintenance for package developers.  The package has been developed since 2001 and is now considered very stable.  This is a cross-platform package implemented in pure R that defines standard S3 classes without any tricks.

This package provides utility methods useful when programming and developing R packages.

Binary alignment (BAM), variant call (BCF), or tabix file import

Martin Morgan, Herv\'e Pag\`es, Valerie Obenchain

This package provides an interface to the 'samtools',
  'bcftools', and 'tabix' utilities (see 'LICENCE') for manipulating
  SAM (Sequence Alignment / Map), binary variant call (BCF) and
  compressed indexed tab-delimited (tabix) files.

methods, IRanges (>= 1.19.11), GenomicRanges (>= 1.13.35),
XVector, Biostrings (>= 2.29.7)

utils, BiocGenerics (>= 0.1.3), zlibbioc, bitops

ShortRead (>= 1.19.10), GenomicFeatures,
TxDb.Dmelanogaster.UCSC.dm3.ensGene, KEGG.db,
TxDb.Hsapiens.UCSC.hg18.knownGene, RNAseqData.HNRNPC.bam.chr14,
BSgenome.Hsapiens.UCSC.hg19, pasillaBamSubset, RUnit, BiocStyle

This package uses the source code of zlib-1.2.5 to create
  libraries for systems that do not have these available via other
  means (most Linux and Mac users should have system-level access to
  zlib, and no direct need for this package). See the vignette for
  instructions on use.