Package: GenomeInfoDb 1.49.1

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_1.49.1.tar.gz
GenomeInfoDb_1.49.1.zip(r-4.7)GenomeInfoDb_1.49.1.zip(r-4.6)GenomeInfoDb_1.49.1.zip(r-4.5)
GenomeInfoDb_1.49.1.tgz(r-4.6-any)GenomeInfoDb_1.49.1.tgz(r-4.5-any)
GenomeInfoDb_1.49.1.tar.gz(r-4.7-any)GenomeInfoDb_1.49.1.tar.gz(r-4.6-any)
GenomeInfoDb_1.49.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
GenomeInfoDb/json (API)

# 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-1.49.1(bioc 3.24)GenomeInfoDb-1.48.0(bioc 3.23)

genetics datarepresentation annotation genomeannotation bioconductor-package core-package

14.15 score 35 stars 335 packages 2.9k scripts 7 mentions 52 exports 14 dependencies

Last updated from:037c38473a. Checks:1 WARNING, 7 ERROR, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	327
linux-devel-x86_64	ERROR	653
source / vignettes	OK	385
linux-release-x86_64	ERROR	639
macos-release-arm64	ERROR	342
macos-oldrel-arm64	ERROR	428
windows-devel	ERROR	553
windows-release	ERROR	563
windows-oldrel	ERROR	645
wasm-release	OK	257

Exports:bsgenomeName 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 isCircular isCircular<-keepSeqlevels keepStandardChromosomes list_ftp_dir listOrganisms loadTaxonomyDb mapGenomeBuilds mapSeqlevels orderSeqlevels provider providerVersion rankSeqlevels registered_NCBI_assemblies registered_UCSC_genomes releaseDate renameSeqlevels saveChromInfoFromNCBI saveChromInfoFromUCSC seqinfo Seqinfo seqinfo<-seqlengths seqlengths<-seqlevels seqlevels<-seqlevels0 seqlevelsInGroup seqlevelsInUse seqlevelsStyle seqlevelsStyle<-seqnames seqnames<-sortSeqlevels standardChromosomes

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

GenomeInfoDb: Introduction to GenomeInfoDb

1 Introduction | 2 Functionality for all existing organisms | 3 Seqinfo objects | 4 Examples | 5 Session Information

Rendered fromGenomeInfoDb.Rnwusingknitr::knitr

Last update: 2025-06-20
Started: 2014-02-14

Submitting your organism to GenomeInfoDb

Background | Support for existing organisms | File format for new organism | Example File | Contacting us with your new file

Rendered fromAccept-organism-for-GenomeInfoDb.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Get chromosome information for an Ensembl species	getChromInfoFromEnsembl
Get chromosome information for an NCBI assembly	getChromInfoFromNCBI registered_NCBI_assemblies saveChromInfoFromNCBI
Get chromosome information for a UCSC genome	getChromInfoFromUCSC get_and_fix_chrom_info_from_UCSC registered_UCSC_genomes saveChromInfoFromUCSC
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
Convenience wrappers to the seqlevels() getter and setter	dropSeqlevels keepSeqlevels keepStandardChromosomes renameSeqlevels 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