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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.

Functions (13)

GenomeDescription-class

GenomeDescription objects

GenomeInfoDb-internals

GenomeInfoDb internals

Seqinfo-class

Seqinfo objects

fetchExtendedChromInfoFromUCSC

Fetching chromosomes info for some of the UCSC genomes

getChromInfoFromEnsembl

Get chromosome information for an Ensembl species

getChromInfoFromNCBI

Get chromosome information for an NCBI assembly

getChromInfoFromUCSC

Get chromosome information for a UCSC genome

loadTaxonomyDb

Return a data.frame that lists the known taxonomy IDs and their corresponding organisms.

mapGenomeBuilds

Mapping between UCSC and Ensembl Genome Builds

rankSeqlevels

Assign sequence IDs to sequence names

Accessing/modifying sequence information

seqlevels-wrappers

Convenience wrappers to the seqlevels() getter and setter

seqlevelsStyle

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

GenomeInfoDb

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

v1.26.7

Artistic-2.0

Authors

Sonali Arora, Martin Morgan, Marc Carlson, H. Pagès

Initial release

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