Package: UCSC.utils 1.3.1
UCSC.utils: Low-level utilities to retrieve data from the UCSC Genome Browser
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.
Authors:
UCSC.utils_1.3.1.tar.gz
UCSC.utils_1.3.1.zip(r-4.5)UCSC.utils_1.3.1.zip(r-4.4)UCSC.utils_1.3.1.zip(r-4.3)
UCSC.utils_1.3.1.tgz(r-4.4-any)UCSC.utils_1.3.1.tgz(r-4.3-any)
UCSC.utils_1.3.1.tar.gz(r-4.5-noble)UCSC.utils_1.3.1.tar.gz(r-4.4-noble)
UCSC.utils_1.3.1.tgz(r-4.4-emscripten)UCSC.utils_1.3.1.tgz(r-4.3-emscripten)
UCSC.utils.pdf |UCSC.utils.html✨
UCSC.utils/json (API)
NEWS
# Install 'UCSC.utils' in R: |
install.packages('UCSC.utils', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/bioconductor/ucsc.utils/issues
On BioConductor:UCSC.utils-1.3.0(bioc 3.21)UCSC.utils-1.2.0(bioc 3.20)
infrastructuregenomeassemblyannotationgenomeannotationdataimportbioconductor-packagecore-package
Last updated 27 days agofrom:6e852499ba. Checks:7 OK. Indexed: yes.
Target | Result | Latest binary |
---|---|---|
Doc / Vignettes | OK | Jan 16 2025 |
R-4.5-win | OK | Jan 16 2025 |
R-4.5-linux | OK | Feb 05 2025 |
R-4.4-win | OK | Jan 16 2025 |
R-4.4-mac | OK | Jan 16 2025 |
R-4.3-win | OK | Jan 16 2025 |
R-4.3-mac | OK | Jan 16 2025 |
Exports:fetch_UCSC_track_dataget_organism_for_UCSC_genomeget_UCSC_chrom_sizeslist_UCSC_genomeslist_UCSC_tracksUCSC_dbselectUCSC.api.url
Dependencies:askpassBiocGenericscurlgenericshttrjsonlitemimeopensslR6S4Vectorssys
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Fetch UCSC track data | fetch_UCSC_track_data |
List UCSC chromosome sizes | get_UCSC_chrom_sizes |
List UCSC genomes | get_organism_for_UCSC_genome list_UCSC_genomes |
List UCSC tracks and associated primary tables | list_UCSC_tracks |
Conveniently retrieve data from the UCSC MariaDB server | UCSC_dbselect |
Get or set the default UCSC API URL | UCSC.api.url |