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.
|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
|lumi||Functions to preprocess Illumina microarray (BeadArray) data. It includes functions of Illumina data input, quality control, variance ...|