Package: GenomeInfoDb 1.43.1
Hervé Pagès
GenomeInfoDb: Utilities for manipulating chromosome names, including modifying them to follow a particular naming style
Contains data and functions that define and allow translation between different chromosome sequence naming conventions (e.g., "chr1" versus "1"), including a function that attempts to place sequence names in their natural, rather than lexicographic, order.
Authors:
GenomeInfoDb_1.43.1.tar.gz
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GenomeInfoDb.pdf |GenomeInfoDb.html✨
GenomeInfoDb/json (API)
NEWS
| # Install 'GenomeInfoDb' in R: |
| install.packages('GenomeInfoDb', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/bioconductor/genomeinfodb/issues
On BioConductor:GenomeInfoDb-1.43.0(bioc 3.21)GenomeInfoDb-1.42.0(bioc 3.20)
geneticsdatarepresentationannotationgenomeannotationbioconductor-packagecore-package
Last updated 8 days agofrom:e24f4388f8. Checks:OK: 1 NOTE: 5 ERROR: 1. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 18 2024 |
| R-4.5-win | NOTE | Nov 18 2024 |
| R-4.5-linux | NOTE | Nov 18 2024 |
| R-4.4-win | NOTE | Nov 18 2024 |
| R-4.4-mac | ERROR | Nov 18 2024 |
| R-4.3-win | NOTE | Nov 18 2024 |
| R-4.3-mac | NOTE | Nov 18 2024 |
Exports:as.data.frameas.data.frame.SeqinfobsgenomeNamecheckCompatibleSeqinfocommonNameDEFAULT_CIRC_SEQSdropSeqlevelsextractSeqlevelsextractSeqlevelsByGroupfetch_assembly_reportfind_NCBI_assembly_ftp_dirgenomegenome<-genomeBuildsGenomeDescriptiongenomeStylesget_and_fix_chrom_info_from_UCSCgetChromInfoFromEnsemblgetChromInfoFromNCBIgetChromInfoFromUCSCintersectisCircularisCircular<-keepSeqlevelskeepStandardChromosomeslist_ftp_dirlistOrganismsloadTaxonomyDbmapGenomeBuildsmapSeqlevelsmergemerge.SeqinfoorderSeqlevelsorganismproviderproviderVersionrankSeqlevelsregistered_NCBI_assembliesregistered_UCSC_genomesreleaseDaterenameSeqlevelsrestoreSeqlevelssaveAssembledMoleculesInfoFromUCSCseqinfoSeqinfoseqinfo<-seqlengthsseqlengths<-seqlevelsseqlevels<-seqlevels0seqlevelsInGroupseqlevelsInUseseqlevelsStyleseqlevelsStyle<-seqnamesseqnames<-showsortSeqlevelsspeciesstandardChromosomessummarysummary.Seqinfoupdate.Seqinfo
Dependencies:askpassBiocGenericscurlgenericsGenomeInfoDbDatahttrIRangesjsonlitemimeopensslR6S4VectorssysUCSC.utils
GenomeInfoDb: Introduction to GenomeInfoDb
Rendered fromGenomeInfoDb.Rnwusingknitr::knitron Nov 18 2024.Last update: 2020-06-27
Started: 2014-02-14
Submitting your organism to GenomeInfoDb
Rendered fromAccept-organism-for-GenomeInfoDb.Rmdusingknitr::rmarkdownon Nov 18 2024.Last update: 2022-12-13
Started: 2022-12-13
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| GenomeDescription objects | bsgenomeName bsgenomeName,GenomeDescription-method class:GenomeDescription commonName commonName,GenomeDescription-method GenomeDescription GenomeDescription-class organism organism,GenomeDescription-method provider provider,GenomeDescription-method providerVersion providerVersion,GenomeDescription-method releaseDate releaseDate,GenomeDescription-method seqinfo,GenomeDescription-method seqnames,GenomeDescription-method show,GenomeDescription-method species species,GenomeDescription-method |
| Get chromosome information for an Ensembl species | getChromInfoFromEnsembl |
| Get chromosome information for an NCBI assembly | getChromInfoFromNCBI registered_NCBI_assemblies |
| Get chromosome information for a UCSC genome | getChromInfoFromUCSC get_and_fix_chrom_info_from_UCSC registered_UCSC_genomes saveAssembledMoleculesInfoFromUCSC |
| Return a data.frame that lists the known taxonomy IDs and their corresponding organisms. | loadTaxonomyDb |
| Mapping between UCSC and Ensembl Genome Builds | genomeBuilds listOrganisms mapGenomeBuilds |
| Utility functions to access NCBI resources | fetch_assembly_report find_NCBI_assembly_ftp_dir NCBI-utils |
| Assign sequence IDs to sequence names | orderSeqlevels rankSeqlevels |
| Accessing/modifying sequence information | genome genome,ANY-method genome<- genome<-,ANY-method isCircular isCircular,ANY-method isCircular<- isCircular<-,ANY-method seqinfo seqinfo<- seqlengths seqlengths,ANY-method seqlengths<- seqlengths<-,ANY-method seqlevels seqlevels,ANY-method seqlevels0 seqlevels<- seqlevels<-,ANY-method seqlevelsInUse seqlevelsInUse,CompressedList-method seqlevelsInUse,Vector-method seqnames seqnames<- sortSeqlevels sortSeqlevels,ANY-method sortSeqlevels,character-method |
| Seqinfo objects | as.data.frame,Seqinfo-method as.data.frame.Seqinfo checkCompatibleSeqinfo class:Seqinfo coerce,data.frame,Seqinfo-method coerce,DataFrame,Seqinfo-method genome,Seqinfo-method genome<-,Seqinfo-method intersect,Seqinfo,Seqinfo-method isCircular,Seqinfo-method isCircular<-,Seqinfo-method length,Seqinfo-method merge,missing,Seqinfo-method merge,NULL,Seqinfo-method merge,Seqinfo,missing-method merge,Seqinfo,NULL-method merge,Seqinfo,Seqinfo-method merge.Seqinfo names,Seqinfo-method names<-,Seqinfo-method Seqinfo Seqinfo-class seqlengths,Seqinfo-method seqlengths<-,Seqinfo-method seqlevels,Seqinfo-method seqlevels<-,Seqinfo-method seqnames,Seqinfo-method seqnames<-,Seqinfo-method show,Seqinfo-method summary,Seqinfo-method summary.Seqinfo update,Seqinfo-method update.Seqinfo [,Seqinfo-method |
| Convenience wrappers to the seqlevels() getter and setter | dropSeqlevels keepSeqlevels keepStandardChromosomes renameSeqlevels restoreSeqlevels seqlevels-wrappers standardChromosomes |
| Conveniently rename the seqlevels of an object according to a given style | extractSeqlevels extractSeqlevelsByGroup genomeStyles mapSeqlevels seqlevelsInGroup seqlevelsStyle seqlevelsStyle,ANY-method seqlevelsStyle,character-method seqlevelsStyle,Seqinfo-method seqlevelsStyle<- seqlevelsStyle<-,ANY-method seqlevelsStyle<-,character-method seqlevelsStyle<-,Seqinfo-method |
