UCSC.utils

Low-level utilities to retrieve data from the UCSC Genome Browser


Bioconductor version: Release (3.19)

A set of low-level utilities to retrieve data from the UCSC Genome Browser. Most functions in the package access the data via the UCSC REST API but some of them query the UCSC MySQL server directly. Note that the primary purpose of the package is to support higher-level functionalities implemented in downstream packages like GenomeInfoDb or txdbmaker.

Author: Hervé Pagès [aut, cre]

Maintainer: Hervé Pagès <hpages.on.github at gmail.com>

Citation (from within R, enter citation("UCSC.utils")):

Installation

To install this package, start R (version "4.4") and enter:


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

BiocManager::install("UCSC.utils")

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("UCSC.utils")
The UCSC.utils package HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Annotation, DataImport, GenomeAnnotation, GenomeAssembly, Infrastructure, Software
Version 1.0.0
In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)
License Artistic-2.0
Depends
Imports methods, stats, httr, jsonlite, S4Vectors
System Requirements
URL https://bioconductor.org/packages/UCSC.utils
Bug Reports https://github.com/Bioconductor/UCSC.utils/issues
See More
Suggests DBI, RMariaDB, GenomeInfoDb, testthat, knitr, rmarkdown, BiocStyle
Linking To
Enhances
Depends On Me
Imports Me GenomeInfoDb, txdbmaker
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package UCSC.utils_1.0.0.tar.gz
Windows Binary (x86_64) UCSC.utils_1.0.0.zip
macOS Binary (x86_64) UCSC.utils_1.0.0.tgz
macOS Binary (arm64) UCSC.utils_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/UCSC.utils
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/UCSC.utils
Bioc Package Browser https://code.bioconductor.org/browse/UCSC.utils/
Package Short Url https://bioconductor.org/packages/UCSC.utils/
Package Downloads Report Download Stats