Bioinformatics and computational biology solutions using R and Bioconductor. (English) Zbl 1142.62100

Gentleman, Robert (ed.); Carey, Vincent J. (ed.); Huber, Wolfgang (ed.); Irizarry, Rafael A. (ed.); Dudoit, Sandrine (ed.)

Statistics for Biology and Health. New York, NY: Springer (ISBN 0-387-25146-4/hbk). xix, 473 p. (2005).

[The articles of this volume will not be indexed individually.]
Publisher’s description: Bioconductor is a widely used open source and open development software project for the analysis and comprehension of data arising from high-throughput experimentation in genomics and molecular biology. Bioconductor is rooted in the open source statistical computing environment R.
This volume’s coverage is broad and ranges across most of the key capabilities of the Bioconductor project, including importation and preprocessing of high-throughput data from microarray, proteomic, and flow cytometry platforms: Curation and delivery of biological metadata for use in statistical modeling and interpretation; Statistical analysis of high-throughput data, including machine learning and visualization; Modeling and visualization of graphs and networks.
The developers of the software, who are in many cases leading academic researchers, jointly authored the chapters. All methods are illustrated with publicly available data, and a major section of the book is devoted to an exposition of fully worked case studies.
This book is more than a static collection of descriptive text, figures, and code examples that were run by the authors to produce the text; it is a dynamic document. The code underlying all of the computations that are shown is made available on a companion website, and readers can reproduce every number, figure, and table on their own computers.

MSC:

62P10	Applications of statistics to biology and medical sciences; meta analysis
92-08	Computational methods for problems pertaining to biology
62-04	Software, source code, etc. for problems pertaining to statistics
92C40	Biochemistry, molecular biology
92-04	Software, source code, etc. for problems pertaining to biology
62-06	Proceedings, conferences, collections, etc. pertaining to statistics
92-06	Proceedings, conferences, collections, etc. pertaining to biology
00B15	Collections of articles of miscellaneous specific interest

Software:

affy; affycomp; affypdnn; affyPLM; Bioconductor; gcrma; hopach; marrayClasses; multtest; R