bedbaser

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see bedbaser.

A BEDbase client

Bioconductor version: 3.21

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 iD ORCID: 0009-0008-0900-8793 , Levi Waldron [aut] ORCID iD ORCID: 0000-0003-2725-0694

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

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

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
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 1.0.4

In Bioconductor since BioC 3.21 (R-4.5) (0.5 years)

License Artistic License 2.0

Depends R (>= 4.5.0)

Imports AnVIL(>= 1.16.0), BiocFileCache, 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)

Linking To

Enhances

Depends On Me

Imports Me

Suggests Me

Links To Me

Build Report Build Report

Package Archives

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

Source Package bedbaser_1.0.4.tar.gz

Windows Binary (x86_64) bedbaser_1.0.3.zip

macOS Binary (x86_64) bedbaser_1.0.4.tgz

macOS Binary (arm64) bedbaser_1.0.4.tgz

Source Repository git clone https://git.bioconductor.org/packages/bedbaser

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/bedbaser

Bioc Package Browser https://code.bioconductor.org/browse/bedbaser/

Package Short Url https://bioconductor.org/packages/bedbaser/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.21 Source Archive