Package: ribiosAnnotation 3.8.0

Jitao David Zhang

ribiosAnnotation: Annotation of Genes, RNAs, and Proteins in 'ribios'

Retrieves annotation information of genomic features including genes, RNAs, and proteins from databases. It supports querying by gene identifiers, gene symbols, UniProt accessions, Ensembl identifiers, and RefSeq identifiers, as well as mapping orthologs across species using NCBI data.

Authors:Jitao David Zhang [aut, cre]

ribiosAnnotation_3.8.0.tar.gz
ribiosAnnotation_3.8.0.zip(r-4.7)ribiosAnnotation_3.8.0.zip(r-4.6)ribiosAnnotation_3.8.0.zip(r-4.5)
ribiosAnnotation_3.8.0.tgz(r-4.6-any)ribiosAnnotation_3.8.0.tgz(r-4.5-any)
ribiosAnnotation_3.8.0.tar.gz(r-4.7-any)ribiosAnnotation_3.8.0.tar.gz(r-4.6-any)
ribiosAnnotation_3.8.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
ribiosAnnotation/json (API)
NEWS

# Install 'ribiosAnnotation' in R:

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

Bug tracker:https://github.com/bedapub/ribiosannotation/issues

Datasets:

commonSpecies - Common species taxonomy IDs
gtibioc - Translation table between GTI and Bioconductor chip type names

On CRAN:

3.40 score 3 packages 28 scripts 43 exports 28 dependencies

Last updated from:331cc913da. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	168
source / vignettes	OK	188
linux-release-x86_64	OK	125
macos-release-arm64	OK	87
macos-oldrel-arm64	OK	89
windows-devel	OK	76
windows-release	OK	85
windows-oldrel	OK	80
wasm-release	OK	104

Exports:annotateAnyIDs annotateEnsemblGeneIDs annotateEnsemblGeneIDsWithEnsembl annotateEnsemblGeneIDsWithHumanOrtholog annotateEnsemblGeneIDsWithNCBI annotateEnsemblGeneIDsWithoutHumanOrtholog annotateGeneIDs annotateGeneIDsWithHumanOrtholog annotateGeneIDsWithoutHumanOrtholog annotateGeneSymbols annotateGeneSymbolsWithHumanOrtholog annotateGeneSymbolsWithoutHumanOrtholog annotateHumanOrthologsWithNCBI annotateNonHumanGenesHumanOrthologsWithNCBI annotateProteinGroups annotateTaxID appendHumanOrthologsWithNCBI bioc2gti connectMongoDB formatIn getAllTaxIDs gti2bioc guessAndAnnotate guessFeatureType humanOrthologsByTaxID isValidFeatureID likeEnsembl likeEnsemblGeneID likeGeneID likeGeneSymbol likeHumanGeneSymbol likeRefSeq likeUniProt loadMongodbSecrets locateSecretsFile majorityLikeHumanGeneSymbol removeEnsemblVersion returnFieldsJson ribiosAnnotationSecretEnvVar ribiosAnnotationSecretFile sortAnnotationByQuery uniprotByTaxID validFeatureIDs

Dependencies:askpass cli cpp11 dplyr generics glue jsonlite lifecycle magrittr mime mongolite openssl pillar pkgconfig purrr R6 ribiosUtils rjson rlang stringi stringr sys tibble tidyr tidyselect utf8 vctrs withr

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Annotate any identifiers	annotateAnyIDs
Annotate Enesembl GeneIDs	annotateEnsemblGeneIDs
Annotate EnsEMBL GeneID with data from EnsEMBL	annotateEnsemblGeneIDsWithEnsembl
Annotate Ensembl GeneIDs while appending human orthologs	annotateEnsemblGeneIDsWithHumanOrtholog
Annotate EnsEMBL GeneID with data from NCBI	annotateEnsemblGeneIDsWithNCBI
Annotate Ensembl GeneIDs with data from both EnsEMBL and NCBI	annotateEnsemblGeneIDsWithoutHumanOrtholog
Annotate Entrez GeneIDs	annotateGeneIDs
Annotate Entrez GeneIDs with the query of human orthologs	annotateGeneIDsWithHumanOrtholog
Annotate Entrez GeneIDs without querying human orthologs	annotateGeneIDsWithoutHumanOrtholog
Annotate GeneSymbols	annotateGeneSymbols
Annotate GeneSymbol with human ortholog	annotateGeneSymbolsWithHumanOrtholog
Annotate gene symbols without human ortholog	annotateGeneSymbolsWithoutHumanOrtholog
Annotate human orthologs with data from NCBI	annotateHumanOrthologsWithNCBI
Annotate human orthologs with data from NCBI	annotateNonHumanGenesHumanOrthologsWithNCBI
Annotate protein groups for proteomics studies	annotateProteinGroups
Annotations of all genes associated with the given TaxID	annotateTaxID
Annotate UniProt accessions or names	annotateUniprotAccession
Append human orthologs to an existing annotation dataframe	appendHumanOrthologsWithNCBI
check single integer Tax ID	checkSingleIntegerTaxId
Common species taxonomy IDs	commonSpecies
Connect to a MongoDB instance	connectMongoDB
Formatting a vector for SQL SELECT query with IN syntax	formatIn
Get all taxonomy ID and scientific names offered by NCBI	getAllTaxIDs
Translate chiptypes between GTI Bioconductor naming conventions	bioc2gti gti2bioc
Translation table between GTI and Bioconductor chip type names	gtibioc
Guess feature ID type by majority voting and annotate them	guessAndAnnotate
Guess feature ID type by majority voting	guessFeatureType
Retrieve human orthologs of genes of another species with its Taxonomy ID	humanOrthologsByTaxID
Whether input character strings are valid feature IDs	isValidFeatureID
Whether input strings look like Entrez GeneIDs	likeEnsembl likeEnsemblGeneID likeGeneID likeGeneSymbol likeHumanGeneSymbol likeRefSeq likeUniProt
Get secrets for MongoDB connections	loadMongodbSecrets
Guess the majority members of a character string look like human gene symbols	majorityLikeHumanGeneSymbol
Remove version suffix from Ensembl IDs	removeEnsemblVersion
Construct a JSON string to indicate returned fields from a MongoDB query	returnFieldsJson
Locate ribiosAnnotation secrets file in JSON	locateSecretsFile ribiosAnnotationSecretEnvVar
ribiosAnnotation secret file	ribiosAnnotationSecretFile
Sort the annotation table by query IDs	sortAnnotationByQuery
Get Uniprot annotation with NCBI Taxonomy ID	uniprotByTaxID
Return valid features in a vector	validFeatureIDs