Package: UCSC.utils 1.1.0
Hervé Pagès
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_1.1.0.tar.gz
UCSC.utils_1.1.0.zip(r-4.5)UCSC.utils_1.1.0.zip(r-4.4)UCSC.utils_1.1.0.zip(r-4.3)
UCSC.utils_1.1.0.tgz(r-4.4-any)UCSC.utils_1.1.0.tgz(r-4.3-any)
UCSC.utils_1.1.0.tar.gz(r-4.5-noble)UCSC.utils_1.1.0.tar.gz(r-4.4-noble)
UCSC.utils_1.1.0.tgz(r-4.4-emscripten)UCSC.utils_1.1.0.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-1.1.0(bioc 3.20)UCSC.utils-1.0.0(bioc 3.19)
Last updated 2 months agofrom:e7cd20fd13
Exports:fetch_UCSC_track_dataget_organism_for_UCSC_genomeget_UCSC_chrom_sizeslist_UCSC_genomeslist_UCSC_tracksUCSC_dbselectUCSC.api.url
Dependencies:askpassBiocGenericscurlhttrjsonlitemimeopensslR6S4Vectorssys
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 |
