Bioinformatics
Robert Gentleman
Programming for
Bioinformatics
R Programming for Bioinformatics
R
Gentleman
From the co-developer of R and lead founder of the Bioconductor project
Due to its data handling and modeling capabilities as well as its exibility, 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 rst-hand experiences as an expert in R, the book
begins with coverage of 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 proling 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.
Features
Covers the fundamentals of the R language and object-oriented •
programming in R
Discusses XML, SOAP, and other data mark-up and web services •
languages and tools
Deals with many of the standard sequence similarity tools that play a •
prominent role in computational biology
Explores the interaction of R with other languages, such as C, FORTRAN, •
Perl, and Python
Explains how to write your own software packages as well as debug and •
prole R code
Contains complete source code on the book’s website •
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