Package: Organism.dplyr 1.33.0

Martin Morgan

Organism.dplyr: dplyr-based Access to Bioconductor Annotation Resources

This package provides an alternative interface to Bioconductor 'annotation' resources, in particular the gene identifier mapping functionality of the 'org' packages (e.g., org.Hs.eg.db) and the genome coordinate functionality of the 'TxDb' packages (e.g., TxDb.Hsapiens.UCSC.hg38.knownGene).

Authors:Martin Morgan [aut, cre], Daniel van Twisk [ctb], Yubo Cheng [aut]

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NEWS

# Install 'Organism.dplyr' in R:

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

Bug tracker:https://github.com/bioconductor/organism.dplyr/issues

On BioConductor:Organism.dplyr-1.33.0(bioc 3.20)Organism.dplyr-1.32.0(bioc 3.19)

bioconductor-package

73 exports 1.38 score 86 dependencies 1 dependents

Last updated 2 months agofrom:35ff40b8c9

Exports:AccnumFilter AliasFilter cds cds_tbl cdsBy cdsBy_tbl CdsChromFilter CdsIdFilter CdsNameFilter CdsStrandFilter columns EnsemblFilter EnsemblprotFilter EnsembltransFilter EnzymeFilter EvidenceallFilter EvidenceFilter ExonChromFilter exons exons_tbl exonsBy exonsBy_tbl ExonStrandFilter fiveUTRsByTranscript fiveUTRsByTranscript_tbl FlybaseCgFilter FlybaseFilter FlybaseProtFilter GeneChromFilter genes genes_tbl GeneStrandFilter GoallFilter GoFilter hg38light intronsByTranscript intronsByTranscript_tbl IpiFilter keys keytypes MapFilter mapIds MgiFilter mm10light OmimFilter OntologyallFilter OntologyFilter orgPackageName PfamFilter PmidFilter promoters promoters_tbl PrositeFilter RefseqFilter select select_tbl seqinfo show src_organism src_ucsc supportedFilters supportedOrganisms threeUTRsByTranscript threeUTRsByTranscript_tbl transcripts transcripts_tbl transcriptsBy transcriptsBy_tbl TxChromFilter TxStrandFilter TxTypeFilter WormbaseFilter ZfinFilter

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

Organism.dplyr

Rendered fromOrganism.dplyr.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2018-01-08
Started: 2017-03-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Filtering src_organism objects	AccnumFilter AliasFilter BasicFilter-class CdsChromFilter CdsIdFilter CdsNameFilter CdsStrandFilter CharacterFilter-class EnsemblFilter EnsemblprotFilter EnsembltransFilter EnzymeFilter EvidenceallFilter EvidenceFilter ExonChromFilter ExonStrandFilter FlybaseCgFilter FlybaseFilter FlybaseProtFilter GeneChromFilter GeneStrandFilter GoallFilter GoFilter IntegerFilter-class IpiFilter MapFilter MgiFilter OmimFilter OntologyallFilter OntologyFilter PfamFilter PmidFilter PrositeFilter RefseqFilter show,BasicFilter-method show,CharacterFilter-method show,IntegerFilter-method supportedFilters,src_organism-method TxChromFilter TxStrandFilter TxTypeFilter WormbaseFilter ZfinFilter
Extract genomic features from src_organism objects	cds cdsBy cdsBy_tbl cds_tbl exons exonsBy exonsBy_tbl exons_tbl fiveUTRsByTranscript fiveUTRsByTranscript_tbl genes genes_tbl Genomic-Extractors intronsByTranscript intronsByTranscript,src_organism-method intronsByTranscript_tbl promoters promoters,src_organism-method promoters_tbl threeUTRsByTranscript threeUTRsByTranscript_tbl transcripts transcriptsBy transcriptsBy_tbl transcripts_tbl
Utilities used in examples, vignettes, and tests	hg38light mm10light
Using the "select" interface on src_organism objects	columns,src_organism-method keys,src_organism-method keytypes,src_organism-method mapIds,src_organism-method select,src_organism-method select_tbl
Create a sqlite database from TxDb and corresponding Org packages	orgPackageName,src_organism-method select_.tbl_organism seqinfo,src_organism-method src_organism src_tbls.src_organism src_ucsc supportedOrganisms tbl.src_organism