lect 16.1 - Basic Introduction to R and Bioconductor. Aedin...

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Basic Introduction to R and Bioconductor. Aedin Culhane 18th Sept 2009 ( aedin@jimmy.harvard.edu ) R (www.r-project.org) is an open source interactive computer system for visualization and analysis of statistical data. Bioconductor (www.bioconductor.org) is a project within R. The Bioconductor project is a source of many resources relevant to data analysis for high-throughput biology. Installing R and Bioconductor 1. Download R from http://www.r-project.org . The primary portal for R is http://cran.r- project.org . Many local mirrors exist and these may provide quicker downloads. R can be download precompiled for Linux, Mac OS and Windows. If you are using Linux, R can be installed using yum install. To install R simply, click on download and select the version appropriate for your operating system. If you use linux, you may be able to use (apt-get install R or yum) depending on the version of Linux you use. For the most users, this precompiled version of R is sufficient. However if you wish to write an extension package for R/Bioconductor, you need to install R from source. Please refer to the R FAQ for directions on this. Windows users will need to install unix tools/perl/latex, please refer to the excellent guide at http://www.murdoch- sutherland.com/Rtools/ . There is also a more (complex) complete description on the bioconductor developers wiki (http://wiki.fhcrc.org/bioc/HowTo/Build_R_on_Windows)
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R Extension Packages On http://cran.r-project.org/ or the mirror you are using. To find out about contributed package please click on the link Contributed extension packages at the bottom of the main download page. This will link to a page with lots of information on contributed packages and to “CRAN Task Views”. CRAN task views, provide many categories of contributed packages and makes installation of these packages simpler.
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For example to install genetics packages type install.packages("ctv") library(ctv) install.views("Genetics") Note these categories contain many packages, for example this Genetics contains 29 packages. Installing Individual Contributed or Extension Packages Although a team of statisticians and programmers maintain R, many independent groups submit contributed packages. This is a very extensive resource of hundreds of programs and will not be install by default. R extensions can be installed easily. R extensions are stored in repositories. Select the package repositories using Packages - Select repositories The R repositories are: CRAN : basic R distribution CRAN (extras)- Contributed R packages. There are several hundred. Bioconductor: The Bioconductor Project produces an open source software framework that will assist biologists and statisticians working in bioinformatics, with primary emphasis on inference using DNA microarrays. A CRAN style R package repository is available via http://www.bioconductor.org/ .
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Omegahat: The Omegahat Project for Statistical Computing provides a variety of open- source software for statistical applications, with special emphasis on web-based software,
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lect 16.1 - Basic Introduction to R and Bioconductor. Aedin...

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