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BiocManager

CRAN Package For Managing Bioconductor Packages

https://github.com/bioconductor/biocmanager

Science Score: 26.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (17.3%) to scientific vocabulary

Keywords

core-services cran r-package

Keywords from Contributors

bioconductor-package core-package bioconductor genomics u24ca289073 bioinformatics hdf5 rhdf5 gene copy-number
Last synced: 6 months ago · JSON representation

Repository

CRAN Package For Managing Bioconductor Packages

Basic Info
Statistics
  • Stars: 76
  • Watchers: 14
  • Forks: 26
  • Open Issues: 21
  • Releases: 24
Topics
core-services cran r-package
Created almost 11 years ago · Last pushed 9 months ago
Metadata Files
Readme Changelog

README.Rmd 

---
output: github_document
---



```{r, include=FALSE}
knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>",
    out.width = "100%"
)
```

# BiocManager BiocManager CRAN landing page


[![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)


## 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

Owner

  • Name: Bioconductor
  • Login: Bioconductor
  • Kind: organization

Software for the analysis and comprehension of high-throughput genomic data

GitHub Events

Total
  • Create event: 5
  • Release event: 1
  • Issues event: 6
  • Watch event: 3
  • Delete event: 3
  • Issue comment event: 8
  • Member event: 1
  • Push event: 16
  • Pull request review comment event: 1
  • Pull request review event: 2
  • Pull request event: 5
  • Fork event: 4
Last Year
  • Create event: 5
  • Release event: 1
  • Issues event: 6
  • Watch event: 3
  • Delete event: 3
  • Issue comment event: 8
  • Member event: 1
  • Push event: 16
  • Pull request review comment event: 1
  • Pull request review event: 2
  • Pull request event: 5
  • Fork event: 4

Committers

Last synced: 8 months ago

All Time
  • Total Commits: 834
  • Total Committers: 16
  • Avg Commits per committer: 52.125
  • Development Distribution Score (DDS): 0.529
Past Year
  • Commits: 24
  • Committers: 2
  • Avg Commits per committer: 12.0
  • Development Distribution Score (DDS): 0.083
Top Committers
Name Email Commits
LiNk-NY m****9@g****m 393
Martin Morgan m****n@r****g 186
Dan Tenenbaum d****a@f****g 110
Martin Morgan m****n@f****g 102
Herve Pages h****s@f****g 11
Hervé Pagès h****s@f****g 8
Daniel Van Twisk d****k@r****g 5
Henrik Bengtsson hb@a****g 5
aoles a****s@g****m 3
Alexandru Mahmoud a****h@g****m 2
Nathaniel Hayden n****n@f****g 2
Valerie Obenchain v****a@f****g 2
vobencha v****n@r****g 2
Brian Deitte b****e@g****m 1
Lori Shepherd L****d@R****g 1
Peter Hickey p****y@g****m 1
Committer Domains (Top 20 + Academic)
fhcrc.org: 5 roswellpark.org: 4 aroma-project.org: 1 fredhutch.org: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 86
  • Total pull requests: 52
  • Average time to close issues: 3 months
  • Average time to close pull requests: 2 months
  • Total issue authors: 52
  • Total pull request authors: 13
  • Average comments per issue: 4.34
  • Average comments per pull request: 1.31
  • Merged pull requests: 33
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 3
  • Pull requests: 6
  • Average time to close issues: 3 months
  • Average time to close pull requests: 2 months
  • Issue authors: 3
  • Pull request authors: 2
  • Average comments per issue: 0.33
  • Average comments per pull request: 0.0
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • mtmorgan (10)
  • LiNk-NY (7)
  • HenrikBengtsson (5)
  • bbimber (3)
  • lwaldron (3)
  • LTLA (3)
  • lshep (3)
  • 15993561663 (3)
  • glin (3)
  • hpages (2)
  • jorainer (2)
  • Jiefei-Wang (2)
  • natyfp (1)
  • jwokaty (1)
  • vjcitn (1)
Pull Request Authors
  • LiNk-NY (32)
  • mtmorgan (7)
  • almahmoud (4)
  • HenrikBengtsson (2)
  • sneumann (2)
  • bdeitte (2)
  • Alanocallaghan (1)
  • aitap (1)
  • Jiefei-Wang (1)
  • rcastelo (1)
  • remlapmot (1)
  • hpages (1)
  • kozo2 (1)
Top Labels
Issue Labels
enhancement (2) question (2) invalid (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 156,237 last-month
  • Total docker downloads: 14,676,699
  • Total dependent packages: 68
  • Total dependent repositories: 334
  • Total versions: 24
  • Total maintainers: 1
cran.r-project.org: BiocManager

Access the Bioconductor Project Package Repository

  • Versions: 24
  • Dependent Packages: 68
  • Dependent Repositories: 334
  • Downloads: 156,237 Last month
  • Docker Downloads: 14,676,699
Rankings
Downloads: 0.7%
Dependent repos count: 0.9%
Dependent packages count: 1.3%
Forks count: 3.6%
Average: 4.9%
Stargazers count: 5.5%
Docker downloads count: 17.3%
Maintainers (1)
marcel.ramos@sph.cuny.edu
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • utils * imports
  • BiocVersion * suggests
  • curl * suggests
  • knitr * suggests
  • remotes * suggests
  • rmarkdown * suggests
  • testthat * suggests
  • withr * suggests
.github/workflows/pkgdown.yaml actions
  • JamesIves/github-pages-deploy-action v4.4.1 composite
  • actions/checkout v3 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite