UCSC.utils
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see UCSC.utils.
Low-level utilities to retrieve data from the UCSC Genome Browser
Bioconductor version: 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("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 | ||
| 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 |