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

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

Bioconductor version: Development (3.20)

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>

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


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

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


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


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

The UCSC.utils package HTML R Script
Reference Manual PDF


biocViews Annotation, DataImport, GenomeAnnotation, GenomeAssembly, Infrastructure, Software
Version 1.1.0
In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)
License Artistic-2.0
Imports methods, stats, httr, jsonlite, S4Vectors
System Requirements
Bug Reports
See More
Suggests DBI, RMariaDB, GenomeInfoDb, testthat, knitr, rmarkdown, BiocStyle
Linking To
Depends On Me
Imports Me GenomeInfoDb, txdbmaker
Suggests Me
Links To Me
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Follow Installation instructions to use this package in your R session.

Source Package UCSC.utils_1.1.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) UCSC.utils_1.1.0.tgz
macOS Binary (arm64) UCSC.utils_1.1.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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