Package: OrganismDbi 1.55.1

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]

OrganismDbi_1.55.1.tar.gz
OrganismDbi_1.55.1.zip(r-4.7)OrganismDbi_1.55.1.zip(r-4.6)OrganismDbi_1.55.1.zip(r-4.5)
OrganismDbi_1.55.1.tgz(r-4.6-any)OrganismDbi_1.55.1.tgz(r-4.5-any)
OrganismDbi_1.55.1.tar.gz(r-4.7-any)OrganismDbi_1.55.1.tar.gz(r-4.6-any)
OrganismDbi_1.55.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
OrganismDbi/json (API)

# Install 'OrganismDbi' in R:

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

On BioConductor:OrganismDbi-1.55.1(bioc 3.24)OrganismDbi-1.54.0(bioc 3.23)

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

annotation infrastructure

7.05 score 35 packages 54 scripts 39 exports 70 dependencies

Last updated from:9880605db7. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	403
linux-devel-x86_64	NOTE	952
source / vignettes	OK	511
linux-release-x86_64	NOTE	1015
macos-release-arm64	NOTE	1444
macos-oldrel-arm64	NOTE	937
windows-devel	NOTE	1057
windows-release	NOTE	796
windows-oldrel	NOTE	930
wasm-release	OK	353

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 promoters resources select selectByRanges selectRangesById seqinfo taxonomyId threeUTRsByTranscript transcripts transcriptsBy tRNAs TxDb TxDb<-

Dependencies:abind AnnotationDbi askpass BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocManager BiocParallel Biostrings bit bit64 bitops blob cachem cigarillo cli codetools cpp11 crayon curl DBI DelayedArray fastmap formatR futile.logger futile.options generics GenomicAlignments GenomicFeatures GenomicRanges glue graph httr IRanges jsonlite KEGGREST lambda.r lattice lifecycle Matrix MatrixGenerics matrixStats memoise mime openssl pkgconfig png R6 RBGL RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors Seqinfo snow SparseArray SummarizedExperiment sys vctrs XML XVector yaml

OrganismDbi: A meta framework for Annotation Packages

Getting started with OrganismDbi | Making your own OrganismDbi packages

Rendered fromOrganismDbi.Rmdusingknitr::rmarkdown

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 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 promoters,MultiDb-method threeUTRsByTranscript,MultiDb-method transcripts,MultiDb-method transcriptsBy,MultiDb-method tRNAs,MultiDb-method