Package: GenomeInfoDb 1.41.1

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:Sonali Arora [aut], Martin Morgan [aut], Marc Carlson [aut], Hervé Pagès [aut, cre], Prisca Chidimma Maduka [ctb], Atuhurira Kirabo Kakopo [ctb], Haleema Khan [ctb], Emmanuel Chigozie Elendu [ctb]

GenomeInfoDb_1.41.1.tar.gz
GenomeInfoDb_1.41.1.zip(r-4.5)GenomeInfoDb_1.41.1.zip(r-4.4)GenomeInfoDb_1.41.1.zip(r-4.3)
GenomeInfoDb_1.41.1.tgz(r-4.4-any)GenomeInfoDb_1.41.1.tgz(r-4.3-any)
GenomeInfoDb_1.41.1.tar.gz(r-4.5-noble)GenomeInfoDb_1.41.1.tar.gz(r-4.4-noble)
GenomeInfoDb_1.41.1.tgz(r-4.4-emscripten)GenomeInfoDb_1.41.1.tgz(r-4.3-emscripten)
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-1.41.1(bioc 3.20)GenomeInfoDb-1.40.1(bioc 3.19)

bioconductor-package

64 exports 13.64 score 13 dependencies 1634 dependents 7 mentions

Last updated 2 months agofrom:4f9eff2bd6

Exports:as.data.frame as.data.frame.Seqinfo bsgenomeName checkCompatibleSeqinfo commonName DEFAULT_CIRC_SEQS dropSeqlevels extractSeqlevels extractSeqlevelsByGroup fetch_assembly_report find_NCBI_assembly_ftp_dir genome genome<-genomeBuilds GenomeDescription genomeStyles get_and_fix_chrom_info_from_UCSC getChromInfoFromEnsembl getChromInfoFromNCBI getChromInfoFromUCSC intersect isCircular isCircular<-keepSeqlevels keepStandardChromosomes list_ftp_dir listOrganisms loadTaxonomyDb mapGenomeBuilds mapSeqlevels merge merge.Seqinfo orderSeqlevels organism provider providerVersion rankSeqlevels registered_NCBI_assemblies registered_UCSC_genomes releaseDate renameSeqlevels restoreSeqlevels saveAssembledMoleculesInfoFromUCSC seqinfo Seqinfo seqinfo<-seqlengths seqlengths<-seqlevels seqlevels<-seqlevels0 seqlevelsInGroup seqlevelsInUse seqlevelsStyle seqlevelsStyle<-seqnames seqnames<-show sortSeqlevels species standardChromosomes summary summary.Seqinfo update.Seqinfo

Dependencies:askpass BiocGenerics curl GenomeInfoDbData httr IRanges jsonlite mime openssl R6 S4Vectors sys UCSC.utils

GenomeInfoDb: Introduction to GenomeInfoDb

Rendered fromGenomeInfoDb.Rnwusingknitr::knitron Jun 22 2024.

Last update: 2020-06-27
Started: 2014-02-14

Submitting your organism to GenomeInfoDb

Sonali Arora, H. Khan

Rendered fromAccept-organism-for-GenomeInfoDb.Rmdusingknitr::rmarkdownon Jun 22 2024.

Last update: 2022-12-13
Started: 2022-12-13

Citation

Development and contributors

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