```{r front, child="front.Rmd", echo=FALSE} ``` ## Installing Bioconductor The one true way to install Bioconductor is by using the `biocLite` script. You get access to this script by sourcing it from the Bioconductor website ```{r biocLite, eval=FALSE} source("http://www.bioconductor.org/biocLite.R") ``` The first time you run the script without arguments, it will install a core set of Bioconductor packages. ```{r biocLite1, eval=FALSE} biocLite() ``` When you run this script, it will autodetect if any of your installed packages are out of date; it will aggressively ask you to update your packages. Because of this, the way you update a Bioconductor installation, is just by running `biocLite()` without any argument. You can check if your installation is fully up-to-date, by running `biocValid()`; it will return `TRUE` if everything is current. You install a new package by using `biocLite` with the package name, for example ```{r biocLite2, eval=FALSE} biocLite("limma") ``` The reason why you want to use `biocLite` - and only this function - to install and update Bioconductor, is because one of the top problems users have is when they mix and match Bioconductor packages from different releases. Using `biocLite` ensures that everything is synchronized. The way you update Bioconductor itself when a new release comes out, is by updating R itself and then run `biocLite`. ## Other Resources - Installation instructions from the [Bioconductor site](http://bioconductor.org/install/). ## Corrections Improvements and corrections to this document can be submitted on its [GitHub](https://github.com/kasperdanielhansen/genbioconductor/blob/master/Rmd/Install_Bioconductor.Rmd) in its [repository](https://github.com/kasperdanielhansen/genbioconductor).