R in a Nutshell, 2nd Edition

Key Bioconductor Packages

The Bioconductor repository contains over 300 packages for working with genetic data. Below is a list of some popular packages, with short descriptions of the classes and functions that they contain.

Category	Package	Description
Loading, pre-processing	aCGH	Classes and functions for array comparative genomic hybridization data. Functions for reading aCGH data from image analysis output files and clone information files and for creating aCGH S3 objects for storing these data. Basic methods for accessing/replacing, subsetting, printing, and plotting aCGH objects.
	affy	Methods for Affymetrix oligonucleotide arrays. Includes class definitions for representing microarray data. Also includes methods for importing data, quality control, and normalization.
	affyQCReport	A package to generate QC reports for Affymetrix array data.
	arrayQuality	Functions for performing print-run and array-level quality assessment.
	gcrma	Background adjustment using sequence information. The main function gcrma converts background-adjusted probe intensities to expression measures using the same normalization and summarization methods as RMA (robust multiarray average).
	limma	limma is an R package for the analysis of gene expression microarray data, especially the use of linear models for analyzing designed experiments and the assessment of differential expression.
	lumi	Functions to preprocess Illumina microarray (BeadArray) data. It includes functions of Illumina data input, quality control, variance ...