Robert Gentleman

Plain and Affectionate Addresses to Youth

Due to its data handling and modeling capabilities as well as its flexibility, R is becoming the most widely used software in bioinformatics. R Programming for Bioinformatics explores the programming skills needed to use this software tool for the solution of bioinformatics and computational biology problems. Drawing on the author’s first-hand experiences as an expert in R, the book begins with coverage on the general properties of the R language, several unique programming aspects of R, and object-oriented programming in R. It presents methods for data input and output as well as database interactions. The author also examines different facets of string handling and manipulations, discusses the interfacing of R with other languages, and describes how to write software packages. He concludes with a discussion on the debugging and profiling of R code. With numerous examples and exercises, this practical guide focuses on developing R programming skills in order to tackle problems encountered in bioinformatics and computational biology.

R Programming for Bioinformatics

Wolfgang Huber

Florian Hahne

Seth Falcon

Bioconductor software has become a standard tool for the analysis and comprehension of data from high-throughput genomics experiments. Its application spans a broad field of technologies used in contemporary molecular biology. In this volume, the authors present a collection of cases to apply Bioconductor tools in the analysis of microarray gene expression data. Topics covered include: (1) import and preprocessing of data from various sources; (2) statistical modeling of differential gene expression; (3) biological metadata; (4) application of graphs and graph rendering; (5) machine learning for clustering and classification problems; (6) gene set enrichment analysis. Each chapter of this book describes an analysis of real data using hands-on example driven approaches. Short exercises help in the learning process and invite more advanced considerations of key topics. The book is a dynamic document. All the code shown can be executed on a local computer, and readers are able to reproduce every computation, figure, and table.

Bioconductor Case Studies

Sandrine Dudoit

Vincent Carey

Rafael Irizarry

Full four-color book. Some of the editors created the Bioconductor project and Robert Gentleman is one of the two originators of R. All methods are illustrated with publicly available data, and a major section of the book is devoted to fully worked case studies. 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.

Robert Gentleman

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