In Bioconductor/BiocManager: Access the Bioconductor Project Package Repository

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BiocManager

Overview

The BiocManager package allows users to install and manage packages from the Bioconductor project, including CRAN packages that depend or import Bioconductor packages. Bioconductor focuses on the statistical analysis and comprehension of high-throughput genomic data.

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

• available() shows all packages associated with a search pattern
• install() installs and/or updates packages either CRAN or Bioconductor
• repositories() shows all package repository URL endpoints
• valid() checks and returns packages that are out-of-date or too new
• version() returns the current Bioconductor version number

Installation

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager", repos = "https://cran.R-project.org")

Usage

Checking Bioconductor version currently in use

BiocManager::version()

Installing Bioconductor packages

BiocManager::install(c("GenomicRanges", "SummarizedExperiment"))

Verifying a valid Bioconductor installation

BiocManager::valid()

More information

Please see the 'Get started' document (package vignette) for more detailed information such as changing Bioconductor version, offline use, and other advanced usage.

Getting help

To report apparent bugs, create a minimal and reproducible example on GitHub.

Bioconductor/BiocManager documentation built on April 12, 2024, 5:58 p.m.