Introduction to Bioconductor exercises

Installing Bioconductor packages

These exercises will run us through the installation of some key packages.

1. Install the Biostrings package

install.packages("BiocManager")

## Installing package into '/usr/local/lib/R/host-site-library'
## (as 'lib' is unspecified)

require(BiocManager)

## Loading required package: BiocManager

BiocManager::install("Biostrings",update = FALSE)

## 'getOption("repos")' replaces Bioconductor standard repositories, see
## '?repositories' for details
## 
## replacement repositories:
##     CRAN: https://packagemanager.rstudio.com/all/__linux__/focal/latest

## Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.0 (2021-05-18)

## Warning: package(s) not installed when version(s) same as current; use `force = TRUE` to
##   re-install: 'Biostrings'

2. Check your Bioconductor version (should be 3.13)

BiocManager::version()

## [1] '3.13'

3. Install the BSgenome annotation package for mouse UCSC mm10 and human UCSC hg19.

BiocManager::install("BSgenome.Hsapiens.UCSC.hg19",update = FALSE)
BiocManager::install("BSgenome.Mmusculus.UCSC.mm10",update = FALSE)