“Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, more than 460 packages, and an active user community.”
We won’t cover the use of Bioconductor in this workshop, but I’ve included some information to get you started if you are interested in exploring Bioconductor and its packages.
Use the biocLite.R script to install Bioconductor packages. To install a particular package, e.g., limma, type the following in an R command window:
source("http://bioconductor.org/biocLite.R") # downloads the latest bioconductor script/repos
biocLite("limma")
To install a selection of core Bioconductor packages, use:
biocLite()
Packages and their dependencies installed by this usage are: affy, affydata, affyPLM, affyQCReport, annaffy, annotate, Biobase, biomaRt, Biostrings, DynDoc, gcrma, genefilter, geneplotter, GenomicRanges, hgu95av2.db, limma, marray, multtest, vsn, and xtable.
After downloading and installing these packages, the script prints "Installation complete" and "TRUE". Warning: there are some large packages, the whole set might take a while to download.