Package: cellbaseR 1.37.0

Mohammed OE Abdallah

cellbaseR: Querying annotation data from the high performance Cellbase web

This R package makes use of the exhaustive RESTful Web service API that has been implemented for the Cellabase database. It enable researchers to query and obtain a wealth of biological information from a single database saving a lot of time. Another benefit is that researchers can easily make queries about different biological topics and link all this information together as all information is integrated.

Authors:Mohammed OE Abdallah

cellbaseR_1.37.0.tar.gz
cellbaseR_1.37.0.zip(r-4.7)cellbaseR_1.37.0.zip(r-4.6)cellbaseR_1.37.0.zip(r-4.5)
cellbaseR_1.37.0.tgz(r-4.6-any)cellbaseR_1.37.0.tgz(r-4.5-any)
cellbaseR_1.37.0.tar.gz(r-4.7-any)cellbaseR_1.37.0.tar.gz(r-4.6-any)
cellbaseR_1.37.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
cellbaseR/json (API)

# Install 'cellbaseR' in R:

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

Bug tracker:https://github.com/melsiddieg/cellbaser/issues

On BioConductor:cellbaseR-1.37.0(bioc 3.24)cellbaseR-1.36.0(bioc 3.23)

annotation variantannotation

5.59 score 2 stars 13 scripts 21 exports 54 dependencies

Last updated from:01b61c7a0e. Checks:1 ERROR, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	194
linux-devel-x86_64	OK	318
source / vignettes	OK	282
linux-release-x86_64	OK	308
macos-release-arm64	OK	217
macos-oldrel-arm64	OK	143
windows-devel	OK	169
windows-release	OK	164
windows-oldrel	OK	190
wasm-release	OK	196

Exports:AnnotateVcf CellBaseParam CellBaseR createGeneModel getCellBase getCellBaseResourceHelp getChromosomeInfo getClinical getConservationByRegion getGene getGeneInfo getMeta getProtein getProteinInfo getRegion getRegulatoryByRegion getTranscript getTranscriptByGene getVariant getVariantAnnotation getXref

Dependencies:askpass BH BiocGenerics BiocParallel Biostrings bitops cli codetools cpp11 crayon curl data.table doParallel dplyr foreach formatR futile.logger futile.options generics GenomicRanges glue httr IRanges iterators jsonlite lambda.r lifecycle magrittr mime openssl pbapply pillar pkgconfig purrr R.methodsS3 R.oo R.utils R6 Rhtslib rlang Rsamtools S4Vectors Seqinfo snow stringi stringr sys tibble tidyr tidyselect utf8 vctrs withr XVector

Simplifying Genomic Annotations in R

Rendered fromcellbaseR.Rmdusingknitr::rmarkdown

Last update: 2023-11-23
Started: 2017-10-08

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
cellbaseR	cellbaseR-package cellbaseR
AnnotateVcf	AnnotateVcf AnnotateVcf,CellBaseR-method
A Constructor for the CellBaseParam Object	CellBaseParam
CellBaseParam Class	CellBaseParam-class
CellBaseR	CellBaseR
CellBaseR Class	CellBaseR-class
createGeneModel	createGeneModel
getCellBase	getCellBase getCellBase,CellBaseR-method
getCellBaseResourceHelp	getCellBaseResourceHelp
getChromosomeInfo	getChromosomeInfo getChromosomeInfo,CellBaseR-method
getClinical	getClinical getClinical,CellBaseR-method
getConservationByRegion	getConservationByRegion
getGene	getGene getGene,CellBaseR-method
getGeneInfo	getGeneInfo
getMeta	getMeta getMeta,CellBaseR-method
getProtein	getProtein getProtein,CellBaseR-method
getProteinInfo	getProteinInfo
getRegion	getRegion getRegion,CellBaseR-method
getRegulatoryByRegion	getRegulatoryByRegion
getTranscript	getTranscript getTranscript,CellBaseR-method
getTranscriptByGene	getTranscriptByGene
getVariant	getVariant getVariant,CellBaseR-method
getVariantAnnotation	getVariantAnnotation
getXref	getXref getXref,CellBaseR-method