https://github.com/Bioconductor/BiocManager
CRAN Package For Managing Bioconductor Packages
https://github.com/Bioconductor/BiocManager
core-services cran r-package
Last synced: 4 months ago
JSON representation
CRAN Package For Managing Bioconductor Packages
- Host: GitHub
- URL: https://github.com/Bioconductor/BiocManager
- Owner: Bioconductor
- Created: 2015-04-15T01:04:01.000Z (almost 10 years ago)
- Default Branch: devel
- Last Pushed: 2024-08-27T21:33:12.000Z (8 months ago)
- Last Synced: 2024-11-30T04:03:34.528Z (5 months ago)
- Topics: core-services, cran, r-package
- Language: R
- Homepage: http://bioconductor.github.io/BiocManager/
- Size: 8.2 MB
- Stars: 73
- Watchers: 16
- Forks: 24
- Open Issues: 23
-
Metadata Files:
- Readme: README.Rmd
- Changelog: NEWS
Awesome Lists containing this project
- jimsghstars - Bioconductor/BiocManager - CRAN Package For Managing Bioconductor Packages (R)
README
---
output: github_document
---
```{r, include=FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
out.width = "100%"
)
```
# BiocManager
[](https://cran.r-project.org/package=BiocManager)
[](https://github.com/Bioconductor/BiocManager/releases)
[](https://cran.r-project.org/package=BiocManager)
## 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* `valid()` checks and returns packages that are out-of-date or too new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