GenomeInfoDb v1.8.3

Utilities for manipulating chromosome and other 'seqname' identifiers

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.

Functions in GenomeInfoDb

Name Description
GenomeDescription-class GenomeDescription objects
speciesMap Species Mapper object and/or list of valid taxonomy Ids
rankSeqlevels Assign sequence IDs to sequence names
available.species Returns a data.frame that lists the available species strings and their taxonomy Ids.
fetchExtendedChromInfoFromUCSC Fetching chromosomes info for some of the UCSC genomes
Seqinfo-class Seqinfo objects
seqinfo Accessing/modifying sequence information
seqlevelsStyle Conveniently rename the seqlevels of an object according to a given style
seqlevels-wrappers Convenience wrappers to the seqlevels() getter and setter
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Encoding UTF-8
biocViews Genetics, DataRepresentation, Annotation, GenomeAnnotation
License Artistic-2.0
Collate utils.R rankSeqlevels.R assembly-utils.R taxIDSpeciesLookup.R fetchExtendedChromInfoFromUCSC.R fetchSequenceInfo.R seqinfo.R seqlevelsStyle.R seqlevels-wrappers.R Seqinfo-class.R GenomeDescription-class.R zzz.R
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