October 2012
Beginner to intermediate
721 pages
21h 38m
English
Content preview from R in a Nutshell, 2nd Edition
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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 ... |
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