# Utilities for manipulating chromosome names, including modifying them to follow a particular naming style

## Documentation for package ‘GenomeInfoDb’ version 1.40.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G I K L M N O P R S U misc

## -- A --

as.data.frame-method | Seqinfo objects
as.data.frame.Seqinfo | Seqinfo objects

## -- B --

bsgenomeName | GenomeDescription objects
bsgenomeName-method | GenomeDescription objects

## -- C --

checkCompatibleSeqinfo | Seqinfo objects
class:GenomeDescription | GenomeDescription objects
class:Seqinfo | Seqinfo objects
coerce-method | Seqinfo objects
commonName | GenomeDescription objects
commonName-method | GenomeDescription objects

## -- D --

dropSeqlevels | Convenience wrappers to the seqlevels() getter and setter

## -- E --

extractSeqlevels | Conveniently rename the seqlevels of an object according to a given style
extractSeqlevelsByGroup | Conveniently rename the seqlevels of an object according to a given style

## -- F --

fetch_assembly_report | Utility functions to access NCBI resources
find_NCBI_assembly_ftp_dir | Utility functions to access NCBI resources

## -- G --

genome | Accessing/modifying sequence information
genome-method | Seqinfo objects
genome-method | Accessing/modifying sequence information
genome<- | Accessing/modifying sequence information
genome<--method | Seqinfo objects
genome<--method | Accessing/modifying sequence information
genomeBuilds | Mapping between UCSC and Ensembl Genome Builds
GenomeDescription | GenomeDescription objects
GenomeDescription-class | GenomeDescription objects
genomeStyles | Conveniently rename the seqlevels of an object according to a given style
getChromInfoFromEnsembl | Get chromosome information for an Ensembl species
getChromInfoFromNCBI | Get chromosome information for an NCBI assembly
getChromInfoFromUCSC | Get chromosome information for a UCSC genome
get_and_fix_chrom_info_from_UCSC | Get chromosome information for a UCSC genome

## -- I --

intersect-method | Seqinfo objects
isCircular | Accessing/modifying sequence information
isCircular-method | Seqinfo objects
isCircular-method | Accessing/modifying sequence information
isCircular<- | Accessing/modifying sequence information
isCircular<--method | Seqinfo objects
isCircular<--method | Accessing/modifying sequence information

## -- K --

keepSeqlevels | Convenience wrappers to the seqlevels() getter and setter
keepStandardChromosomes | Convenience wrappers to the seqlevels() getter and setter

## -- L --

length-method | Seqinfo objects
listOrganisms | Mapping between UCSC and Ensembl Genome Builds
loadTaxonomyDb | Return a data.frame that lists the known taxonomy IDs and their corresponding organisms.

## -- M --

mapGenomeBuilds | Mapping between UCSC and Ensembl Genome Builds
mapSeqlevels | Conveniently rename the seqlevels of an object according to a given style
merge-method | Seqinfo objects
merge.Seqinfo | Seqinfo objects

## -- N --

names-method | Seqinfo objects
names<--method | Seqinfo objects
NCBI-utils | Utility functions to access NCBI resources

## -- O --

orderSeqlevels | Assign sequence IDs to sequence names
organism | GenomeDescription objects
organism-method | GenomeDescription objects

## -- P --

provider | GenomeDescription objects
provider-method | GenomeDescription objects
providerVersion | GenomeDescription objects
providerVersion-method | GenomeDescription objects

## -- R --

rankSeqlevels | Assign sequence IDs to sequence names
registered_NCBI_assemblies | Get chromosome information for an NCBI assembly
registered_UCSC_genomes | Get chromosome information for a UCSC genome
releaseDate | GenomeDescription objects
releaseDate-method | GenomeDescription objects
renameSeqlevels | Convenience wrappers to the seqlevels() getter and setter
restoreSeqlevels | Convenience wrappers to the seqlevels() getter and setter

## -- S --

saveAssembledMoleculesInfoFromUCSC | Get chromosome information for a UCSC genome
Seqinfo | Seqinfo objects
seqinfo | Accessing/modifying sequence information
Seqinfo-class | Seqinfo objects
seqinfo-method | GenomeDescription objects
seqinfo<- | Accessing/modifying sequence information
seqlengths | Accessing/modifying sequence information
seqlengths-method | Seqinfo objects
seqlengths-method | Accessing/modifying sequence information
seqlengths<- | Accessing/modifying sequence information
seqlengths<--method | Seqinfo objects
seqlengths<--method | Accessing/modifying sequence information
seqlevels | Accessing/modifying sequence information
seqlevels-method | Seqinfo objects
seqlevels-method | Accessing/modifying sequence information
seqlevels-wrappers | Convenience wrappers to the seqlevels() getter and setter
seqlevels0 | Accessing/modifying sequence information
seqlevels<- | Accessing/modifying sequence information
seqlevels<--method | Seqinfo objects
seqlevels<--method | Accessing/modifying sequence information
seqlevelsInGroup | Conveniently rename the seqlevels of an object according to a given style
seqlevelsInUse | Accessing/modifying sequence information
seqlevelsInUse-method | Accessing/modifying sequence information
seqlevelsStyle | Conveniently rename the seqlevels of an object according to a given style
seqlevelsStyle-method | Conveniently rename the seqlevels of an object according to a given style
seqlevelsStyle<- | Conveniently rename the seqlevels of an object according to a given style
seqlevelsStyle<--method | Conveniently rename the seqlevels of an object according to a given style
seqnames | Accessing/modifying sequence information
seqnames-method | GenomeDescription objects
seqnames-method | Seqinfo objects
seqnames<- | Accessing/modifying sequence information
seqnames<--method | Seqinfo objects
show-method | GenomeDescription objects
show-method | Seqinfo objects
sortSeqlevels | Accessing/modifying sequence information
sortSeqlevels-method | Accessing/modifying sequence information
species | GenomeDescription objects
species-method | GenomeDescription objects
standardChromosomes | Convenience wrappers to the seqlevels() getter and setter
summary-method | Seqinfo objects
summary.Seqinfo | Seqinfo objects

## -- U --

update-method | Seqinfo objects
update.Seqinfo | Seqinfo objects

## -- misc --

[-method | Seqinfo objects