GenomeInfoDb: Utilities for manipulating chromosome and other 'seqname' identifiers

Share:

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.

Author
Sonali Arora, Martin Morgan, Marc Carlson, H. Pag├Ęs
Date of publication
None
Maintainer
Bioconductor Package Maintainer <maintainer@bioconductor.org>
License
Artistic-2.0
Version
1.10.1

View on Bioconductor

Man pages

available.species
Returns a data.frame that lists the available species strings...
fetchExtendedChromInfoFromUCSC
Fetching chromosomes info for some of the UCSC genomes
GenomeDescription-class
GenomeDescription objects
mapGenomeBuilds
Mapping between UCSC and Ensembl Genome Builds
rankSeqlevels
Assign sequence IDs to sequence names
seqinfo
Accessing/modifying sequence information
Seqinfo-class
Seqinfo objects
seqlevelsStyle
Conveniently rename the seqlevels of an object according to a...
seqlevels-wrappers
Convenience wrappers to the seqlevels() getter and setter
speciesMap
Species Mapper object and/or list of valid taxonomy Ids

Files in this package

GenomeInfoDb/DESCRIPTION
GenomeInfoDb/NAMESPACE
GenomeInfoDb/NEWS
GenomeInfoDb/R
GenomeInfoDb/R/GenomeDescription-class.R
GenomeInfoDb/R/Seqinfo-class.R
GenomeInfoDb/R/assembly-utils.R
GenomeInfoDb/R/available.species.R
GenomeInfoDb/R/fetchExtendedChromInfoFromUCSC.R
GenomeInfoDb/R/fetchSequenceInfo.R
GenomeInfoDb/R/mapGenomeBuilds.R
GenomeInfoDb/R/rankSeqlevels.R
GenomeInfoDb/R/seqinfo.R
GenomeInfoDb/R/seqlevels-wrappers.R
GenomeInfoDb/R/seqlevelsStyle.R
GenomeInfoDb/R/utils.R
GenomeInfoDb/R/zzz.R
GenomeInfoDb/build
GenomeInfoDb/build/vignette.rds
GenomeInfoDb/data
GenomeInfoDb/data/datalist
GenomeInfoDb/data/specData.rda
GenomeInfoDb/data/speciesMap.rda
GenomeInfoDb/data/validTaxIds.rda
GenomeInfoDb/inst
GenomeInfoDb/inst/doc
GenomeInfoDb/inst/doc/Accept-organism-for-GenomeInfoDb.R
GenomeInfoDb/inst/doc/Accept-organism-for-GenomeInfoDb.Rnw
GenomeInfoDb/inst/doc/Accept-organism-for-GenomeInfoDb.pdf
GenomeInfoDb/inst/doc/GenomeInfoDb.R
GenomeInfoDb/inst/doc/GenomeInfoDb.Rnw
GenomeInfoDb/inst/doc/GenomeInfoDb.pdf
GenomeInfoDb/inst/extdata
GenomeInfoDb/inst/extdata/dataFiles
GenomeInfoDb/inst/extdata/dataFiles/Arabidopsis_thaliana.txt
GenomeInfoDb/inst/extdata/dataFiles/Caenorhabditis_elegans.txt
GenomeInfoDb/inst/extdata/dataFiles/Canis_familiaris.txt
GenomeInfoDb/inst/extdata/dataFiles/Cyanidioschyzon_merolae.txt
GenomeInfoDb/inst/extdata/dataFiles/Drosophila_melanogaster.txt
GenomeInfoDb/inst/extdata/dataFiles/Homo_sapiens.txt
GenomeInfoDb/inst/extdata/dataFiles/Mus_musculus.txt
GenomeInfoDb/inst/extdata/dataFiles/Oryza_sativa.txt
GenomeInfoDb/inst/extdata/dataFiles/Populus_trichocarpa.txt
GenomeInfoDb/inst/extdata/dataFiles/Rattus_norvegicus.txt
GenomeInfoDb/inst/extdata/dataFiles/Saccharomyces_cerevisiae.txt
GenomeInfoDb/inst/extdata/dataFiles/Zea_mays.txt
GenomeInfoDb/inst/extdata/dataFiles/genomeMappingTbl.csv
GenomeInfoDb/inst/unitTests
GenomeInfoDb/inst/unitTests/test_Seqinfo-class.R
GenomeInfoDb/inst/unitTests/test_mapGenomeBuilds.R
GenomeInfoDb/inst/unitTests/test_seqlevels-wrappers.R
GenomeInfoDb/inst/unitTests/test_seqlevelsStyle.R
GenomeInfoDb/inst/unitTests/test_utils.R
GenomeInfoDb/man
GenomeInfoDb/man/GenomeDescription-class.Rd
GenomeInfoDb/man/Seqinfo-class.Rd
GenomeInfoDb/man/available.species.Rd
GenomeInfoDb/man/fetchExtendedChromInfoFromUCSC.Rd
GenomeInfoDb/man/mapGenomeBuilds.Rd
GenomeInfoDb/man/rankSeqlevels.Rd
GenomeInfoDb/man/seqinfo.Rd
GenomeInfoDb/man/seqlevels-wrappers.Rd
GenomeInfoDb/man/seqlevelsStyle.Rd
GenomeInfoDb/man/speciesMap.Rd
GenomeInfoDb/tests
GenomeInfoDb/tests/run_unitTests.R
GenomeInfoDb/vignettes
GenomeInfoDb/vignettes/Accept-organism-for-GenomeInfoDb.Rnw
GenomeInfoDb/vignettes/GenomeInfoDb.Rnw