bedbaser

This is the development version of bedbaser; for the stable release version, see bedbaser.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21

A BEDbase client

Bioconductor version: Development (3.24)

A client for BEDbase. bedbaser provides access to the API at api.bedbase.org. It also includes convenience functions to import BED files into GRanges objects and BEDsets into GRangesLists.

Author: Andres Wokaty [aut, cre] ORCID: 0009-0008-0900-8793 , Levi Waldron [aut] ORCID: 0000-0003-2725-0694 , NCI [fnd] (GrantNo.: U24CA289073)

Maintainer: Andres Wokaty <andres.wokaty at sph.cuny.edu>

Citation (from within R, enter citation("bedbaser")):

Andres Wokaty, Levi Waldron. bedbaser: A BEDbase client. doi:10.18129/B9.bioc.bedbaser, R package version 1.5.1, https://bioconductor.org/packages/bedbaser.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

BiocManager::install("bedbaser")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("bedbaser")

bedbaser	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, Software, ThirdPartyClient
Version	1.5.1
In Bioconductor since	BioC 3.21 (R-4.5) (1.5 years)
License	Artistic License 2.0
Depends	R (>= 4.5.0)
Imports	AnVIL (>= 1.16.0), BiocFileCache, curl, dplyr, GenomeInfoDb, GenomicRanges, httr, methods, purrr, rtracklayer, rlang, R.utils, stats, stringr, tibble, tidyr, tools, utils
System Requirements
URL	https://github.com/waldronlab/bedbaser
Bug Reports	https://github.com/waldronlab/bedbaser/issues

Suggests	BiocStyle, knitr, liftOver, testthat (>= 3.0.0), withr
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	bedbaser_1.5.1.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)	bedbaser_1.5.1.tgz
macOS Binary (sonoma-arm64)	bedbaser_1.5.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/bedbaser
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/bedbaser
Package Short Url	https://bioconductor.org/packages/bedbaser/
Package Downloads Report	Download Stats