Package: OrganismDbi 1.49.0

Bioconductor Package Maintainer

OrganismDbi: Software to enable the smooth interfacing of different database packages

The package enables a simple unified interface to several annotation packages each of which has its own schema by taking advantage of the fact that each of these packages implements a select methods.

Authors:Marc Carlson [aut], Martin Morgan [aut], Valerie Obenchain [aut], Aliyu Atiku Mustapha [ctb], Bioconductor Package Maintainer [cre]

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

# Install 'OrganismDbi' in R:

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

On BioConductor:OrganismDbi-1.47.0(bioc 3.20)OrganismDbi-1.46.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

annotation infrastructure

7.45 score 35 packages 34 scripts 5.3k downloads 40 exports 96 dependencies

Last updated 26 days agofrom:223f33d005. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win	NOTE	Oct 31 2024
R-4.5-linux	NOTE	Oct 30 2024
R-4.4-win	NOTE	Oct 31 2024
R-4.4-mac	NOTE	Oct 31 2024
R-4.3-win	NOTE	Oct 31 2024
R-4.3-mac	NOTE	Oct 31 2024

Exports:asBED asGFF cds cdsBy columns dbconn dbfile distance exons exonsBy extractUpstreamSeqs fiveUTRsByTranscript genes getTxDbIfAvailable intronsByTranscript isActiveSeq isActiveSeq<-keys keytypes makeOrganismDbFromBiomart makeOrganismDbFromTxDb makeOrganismDbFromUCSC makeOrganismPackage mapIds mapToTranscripts metadata microRNAs promoters resources select selectByRanges selectRangesById seqinfo taxonomyId threeUTRsByTranscript transcripts transcriptsBy tRNAs TxDb TxDb<-

Dependencies:abind AnnotationDbi askpass BH Biobase BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel biomaRt Biostrings bit bit64 bitops blob cachem cli codetools cpp11 crayon curl DBI dbplyr DelayedArray digest dplyr fansi fastmap filelock formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges glue graph hms httr httr2 IRanges jsonlite KEGGREST lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pillar pkgconfig plogr png prettyunits progress purrr R6 rappdirs RBGL RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect txdbmaker UCSC.utils utf8 vctrs withr XML xml2 XVector yaml zlibbioc

OrganismDbi: A meta framework for Annotation Packages

Marc Carlson, Aliyu Atiku Mustapha

Rendered fromOrganismDbi.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2023-04-18
Started: 2023-04-18

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Make a OrganismDb object from annotations available on a BioMart database	makeOrganismDbFromBiomart
Make an OrganismDb object from an existing TxDb object.	makeOrganismDbFromTxDb
Make a OrganismDb object from annotations available at the UCSC Genome Browser	makeOrganismDbFromUCSC
Making OrganismDb packages from annotation packages.	makeOrganismPackage
Map range coordinates between transcripts and genome space	mapToTranscripts,ANY,MultiDb-method
MultiDb and OrganismDb objects	class:MultiDb class:OrganismDb columns,MultiDb-method dbconn,MultiDb-method dbfile,MultiDb-method keys,MultiDb-method keytypes,MultiDb-method mapIds,MultiDb-method metadata,MultiDb-method MultiDb MultiDb-class OrganismDb OrganismDb-class resources resources,MultiDb-method select,MultiDb-method selectByRanges selectByRanges,MultiDb-method selectRangesById selectRangesById,MultiDb-method seqinfo,MultiDb-method taxonomyId,MultiDb-method TxDb TxDb,OrganismDb-method TxDb<- TxDb<-,OrganismDb-method
Extract genomic features from an object	asBED,MultiDb-method asGFF,MultiDb-method cds,MultiDb-method cdsBy,MultiDb-method distance,GenomicRanges,MultiDb-method exons,MultiDb-method exonsBy,MultiDb-method extractTranscriptSeqs,BSgenome-method extractUpstreamSeqs,MultiDb-method fiveUTRsByTranscript,MultiDb-method genes,MultiDb-method getTxDbIfAvailable getTxDbIfAvailable,MultiDb-method intronsByTranscript,MultiDb-method isActiveSeq,MultiDb-method isActiveSeq<-,MultiDb-method microRNAs,MultiDb-method promoters,MultiDb-method threeUTRsByTranscript,MultiDb-method transcripts,MultiDb-method transcriptsBy,MultiDb-method tRNAs,MultiDb-method