Package: bedbaser 0.99.23

Andres Wokaty

bedbaser: A BEDbase client

A client for BEDbase. bedbaser provides access to the API at api.bedbase.org. It also includes convenience functions to import BED files into GRanges objects and BEDsets into GRangesLists.

Authors:Andres Wokaty [aut, cre], Levi Waldron [aut]

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bedbaser.pdf |bedbaser.html✨
bedbaser/json (API)
NEWS

# Install 'bedbaser' in R:

install.packages('bedbaser', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/waldronlab/bedbaser/issues

On BioConductor:bedbaser-0.99.23(bioc 3.21)

software dataimport thirdpartyclient u24ca289073

4.00 score 1 stars 3 scripts 94 downloads 15 exports 115 dependencies

Last updated 2 months agofrom:466392b408. Checks:1 ERROR, 8 WARNING. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	FAIL	Mar 24 2025
R-4.5-win	WARNING	Mar 24 2025
R-4.5-mac	WARNING	Mar 24 2025
R-4.5-linux	WARNING	Mar 24 2025
R-4.4-win	WARNING	Mar 24 2025
R-4.4-mac	WARNING	Mar 24 2025
R-4.4-linux	WARNING	Mar 24 2025
R-4.3-win	WARNING	Mar 24 2025
R-4.3-mac	WARNING	Mar 24 2025

Exports:bb_bed_text_search bb_beds_in_bedset bb_example bb_list_beds bb_list_bedsets bb_metadata bb_save bb_to_granges bb_to_grangeslist BEDbase getCache operations schemas setCache tags

Dependencies:abind AnVIL AnVILBase askpass base64enc BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob bslib cachem cli codetools commonmark cpp11 crayon crosstalk curl DBI dbplyr DelayedArray digest dplyr DT evaluate fansi fastmap filelock fontawesome formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges glue highr htmltools htmlwidgets httpuv httr httr2 IRanges jquerylib jsonlite knitr lambda.r later lattice lazyeval lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime miniUI openssl pillar pkgconfig plogr promises purrr R.methodsS3 R.oo R.utils R6 rapiclient rappdirs Rcpp RCurl restfulr Rhtslib rjson rlang rmarkdown Rsamtools RSQLite rtracklayer S4Arrays S4Vectors sass shiny snow sourcetools SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex UCSC.utils utf8 vctrs withr xfun XML xtable XVector yaml

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Search BED files by text	bb_bed_text_search
Get BEDs associated with BEDset	bb_beds_in_bedset
Get the example BED file or BEDset with metadata	bb_example
List BEDs	bb_list_beds
List BEDsets	bb_list_bedsets
Get metadata for a BED file or BEDset	bb_metadata
Save a BED file or BEDset to a path given an id	bb_save
Create a GRanges object given a BED id	bb_to_granges
Create a GRangesList object given a BEDset id	bb_to_grangeslist
An R client for BEDbase	BEDbase getCache setCache
BEDbase class	.BEDbase BEDbase-class
Return cache path	getCache,BEDbase-method
Display API functions	operations,BEDbase-method
Display bedhost API schemas	schemas,BEDbase-method
Set cache along path	setCache,BEDbase-method
Display functions for a tag	tags,BEDbase-method