Installing and Managing Bioconductor Packages

Marcel Ramos1 and Martin Morgan1

1Roswell Park Comprehensive Cancer Center, Buffalo, NY

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1 Introduction

    Use the BiocManager package to install and manage packages from the Bioconductor project for the statistical analysis and comprehension of high-throughput genomic data.

    Current Bioconductor packages are available on a 'relaease' version intended for every-day use, and a 'devel' version where new features are introduced.A new release version is created every six months. Using the BiocManager package helps users install packages from the same release.

2 Basic use 

    install.packages("BiocManager")

install Bioconductor (or CRAN) packages with

BiocManager::install(c("GenomicRanges", "Organism.dplyr"))

installed packages canbe updated to their current version with

BiocManager::install()

Use version() to discover the version of Bioconductor currently in use

BiocManager::version()

Bioconductor packages work best when they are from same release.Use valid() to identify packages that are out-of -date or from unexpected version.

BiocManager::valid()

valid() returns an objects that can be queried for detailed information about invalid packages