README.Rmd

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# BiocManager

<!-- badges: start -->
[![CRAN status](https://www.r-pkg.org/badges/version/BiocManager)](https://cran.r-project.org/package=BiocManager)
[![CRAN release](http://www.r-pkg.org/badges/version-last-release/BiocManager)](https://github.com/Bioconductor/BiocManager/releases)
[![CRAN downloads](http://cranlogs.r-pkg.org/badges/BiocManager)](https://cran.r-project.org/package=BiocManager)
<!-- badges: end -->

## Overview

The `BiocManager` package allows users to install and manage packages
from the _[Bioconductor][1]_ 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* `valid()` checks and returns packages that are out-of-date or too new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

```{r, eval = FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager", repos = "https://cran.R-project.org")
```

## Usage

### Checking Bioconductor version currently in use

```{r, message=FALSE}
BiocManager::version()
```

### Installing Bioconductor packages

```{r, eval=FALSE}
BiocManager::install(c("GenomicRanges", "SummarizedExperiment"))
```

### Verifying a valid Bioconductor installation

```{r}
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][2].

[1]: https://bioconductor.org
[2]: https://github.com/Bioconductor/BiocManager/issues