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

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Documentation for package ‘GenomeInfoDb’ version 1.30.1

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

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

-- A --

as.data.frame-method	Seqinfo objects
as.data.frame.Seqinfo	Seqinfo objects
available.species	Return a data.frame that lists the known taxonomy IDs and their corresponding organisms.

-- 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 --

fetchExtendedChromInfoFromUCSC

Fetching chromosomes info for some of the UCSC genomes

-- 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

-- 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

-- N --

names-method	Seqinfo objects
names<--method	Seqinfo objects

-- 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
releaseName	GenomeDescription objects
releaseName-method	GenomeDescription objects
renameSeqlevels	Convenience wrappers to the seqlevels() getter and setter
restoreSeqlevels	Convenience wrappers to the seqlevels() getter and setter

-- S --

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

-- misc --

[-method

Seqinfo objects