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GenomeInfoDb (version 1.8.3)

Utilities for manipulating chromosome and other 'seqname' identifiers

Description

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.

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Version

Version

1.8.3

License

Artistic-2.0

Maintainer

Bioconductor Package Maintainer

Last Published

February 15th, 2017

Functions in GenomeInfoDb (1.8.3)

GenomeDescription-class

GenomeDescription objects

Species Mapper object and/or list of valid taxonomy Ids

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 objects

Accessing/modifying sequence information

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

seqlevels-wrappers

Convenience wrappers to the seqlevels() getter and setter