Package: UnderstandingRBioc
Type: Package
Title: Gaining Deeper Understanding of R / Bioconductor
Version: 0.0.2
Author: Marc Carlson, Valerie Obenchain, Herv\'e Pag\`es, Paul
    Shannon, Dan Tenenbaum, Martin Morgan
Maintainer: Biocore Team c/o BioC user list
        <bioconductor@stat.math.ethz.ch>
License: Artistic-2.0
VignetteBuilder: knitr
Description: This course is directed at intermediate R / Bioconductor
    users who, in an effort to get the most out of high-throughput
    sequence and other analyses, want to understand more about how R
    and Bioconductor work. (1) The course begins by reviewing R data
    types, memory management, and other aspects of internal
    computation. We use this as a basis for understanding how to
    writing, debug, and assess the performance of efficient R code,
    including straight-forward approaches to iteration, vectorization,
    and parallel evaluation. (2) We then explore R objects, especially
    the S4 object system. We learn about how to specify simple and
    more complicated S4 objects, and how to implement essential
    methods for single and multiple dispatch. We use insights from
    performance and the S4 class system to explore strategies for
    efficient representation of large structured data, especially the
    classes in the IRanges, GenomicRanges, VariantAnnotation, and
    Biostrings packages. (3) Availability of programming libraries
    (such as samtools) or performance needs may sometimes point to use
    of C or C++ code integrated into R. We develop some simple C
    functions, and explore use of Rcpp as a relatively painless way to
    incorporate C code. We take a brief look at R's internal data
    representations, and explore how to debug and profile C code. (4)
    Finally, we investigate how R can be used to interact with other
    important resources: data bases; web sites; and visualization
    facilities like shiny. Use of some of these facilities is
    illustrated by packages such as AnnotationDbi and biomaRt.
Suggests: AnnotationDbi, RCurl, RSQLite, RUnit, Rcpp, ShortRead, XML,
        lattice, microbenchmark
Packaged: 2013-10-02 17:07:45 UTC; dtenenba
