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
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manual.pdf |manual.html✨
card.svg |card.png
cellbaseR/json (API)
NEWS

# 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)

annotationvariantannotation

5.48 score 2 stars 7 scripts 374 downloads 21 exports 54 dependencies

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

TargetResultTimeFilesSyslog
bioc-checksERROR176
linux-devel-x86_64OK287
source / vignettesOK317
linux-release-x86_64OK329
macos-release-arm64OK169
macos-oldrel-arm64OK181
windows-develOK173
windows-releaseOK281
windows-oldrelOK208
wasm-releaseOK151

Exports:AnnotateVcfCellBaseParamCellBaseRcreateGeneModelgetCellBasegetCellBaseResourceHelpgetChromosomeInfogetClinicalgetConservationByRegiongetGenegetGeneInfogetMetagetProteingetProteinInfogetRegiongetRegulatoryByRegiongetTranscriptgetTranscriptByGenegetVariantgetVariantAnnotationgetXref

Dependencies:askpassBHBiocGenericsBiocParallelBiostringsbitopsclicodetoolscpp11crayoncurldata.tabledoParalleldplyrforeachformatRfutile.loggerfutile.optionsgenericsGenomicRangesgluehttrIRangesiteratorsjsonlitelambda.rlifecyclemagrittrmimeopensslpbapplypillarpkgconfigpurrrR.methodsS3R.ooR.utilsR6RhtslibrlangRsamtoolsS4VectorsSeqinfosnowstringistringrsystibbletidyrtidyselectutf8vctrswithrXVector

Simplifying Genomic Annotations in R

Mohammed Omar Elsiddieg Abdallah

Rendered fromcellbaseR.Rmdusingknitr::rmarkdownon Jun 02 2026.

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

Readme and manuals

Help Manual

Help pageTopics
cellbaseRcellbaseR-package cellbaseR
AnnotateVcfAnnotateVcf AnnotateVcf,CellBaseR-method
A Constructor for the CellBaseParam ObjectCellBaseParam
CellBaseParam ClassCellBaseParam-class
CellBaseRCellBaseR
CellBaseR ClassCellBaseR-class
createGeneModelcreateGeneModel
getCellBasegetCellBase getCellBase,CellBaseR-method
getCellBaseResourceHelpgetCellBaseResourceHelp
getChromosomeInfogetChromosomeInfo getChromosomeInfo,CellBaseR-method
getClinicalgetClinical getClinical,CellBaseR-method
getConservationByRegiongetConservationByRegion
getGenegetGene getGene,CellBaseR-method
getGeneInfogetGeneInfo
getMetagetMeta getMeta,CellBaseR-method
getProteingetProtein getProtein,CellBaseR-method
getProteinInfogetProteinInfo
getRegiongetRegion getRegion,CellBaseR-method
getRegulatoryByRegiongetRegulatoryByRegion
getTranscriptgetTranscript getTranscript,CellBaseR-method
getTranscriptByGenegetTranscriptByGene
getVariantgetVariant getVariant,CellBaseR-method
getVariantAnnotationgetVariantAnnotation
getXrefgetXref getXref,CellBaseR-method