GenomeInfoDb: 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.

AuthorSonali Arora, Martin Morgan, Marc Carlson, H. Pag├Ęs
Date of publicationNone
MaintainerBioconductor Package Maintainer <maintainer@bioconductor.org>
LicenseArtistic-2.0
Version1.10.3

View on Bioconductor

Functions

as.data.frame,Seqinfo-method Man page
available.species Man page
bsgenomeName Man page
bsgenomeName,GenomeDescription-method Man page
class:GenomeDescription Man page
class:Seqinfo Man page
coerce,data.frame,Seqinfo-method Man page
coerce,DataFrame,Seqinfo-method Man page
commonName Man page
commonName,GenomeDescription-method Man page
dropSeqlevels Man page
extractSeqlevels Man page
extractSeqlevelsByGroup Man page
fetchExtendedChromInfoFromUCSC Man page
genome Man page
genome<- Man page
genome<-,ANY-method Man page
genome,ANY-method Man page
genomeBuilds Man page
GenomeDescription Man page
GenomeDescription-class Man page
genome<-,Seqinfo-method Man page
genome,Seqinfo-method Man page
genomeStyles Man page
intersect,Seqinfo,Seqinfo-method Man page
isCircular Man page
isCircular<- Man page
isCircular<-,ANY-method Man page
isCircular,ANY-method Man page
isCircular<-,Seqinfo-method Man page
isCircular,Seqinfo-method Man page
keepSeqlevels Man page
keepStandardChromosomes Man page
length,Seqinfo-method Man page
listOrganisms Man page
mapGenomeBuilds Man page
mapSeqlevels Man page
merge,missing,Seqinfo-method Man page
merge,NULL,Seqinfo-method Man page
merge,Seqinfo,missing-method Man page
merge,Seqinfo,NULL-method Man page
merge,Seqinfo,Seqinfo-method Man page
names<-,Seqinfo-method Man page
names,Seqinfo-method Man page
orderSeqlevels Man page
organism Man page
organism,GenomeDescription-method Man page
provider Man page
provider,GenomeDescription-method Man page
providerVersion Man page
providerVersion,GenomeDescription-method Man page
rankSeqlevels Man page
releaseDate Man page
releaseDate,GenomeDescription-method Man page
releaseName Man page
releaseName,GenomeDescription-method Man page
renameSeqlevels Man page
restoreSeqlevels Man page
seqinfo Man page
seqinfo<- Man page
Seqinfo Man page
Seqinfo Man page
Seqinfo-class Man page
seqinfo,GenomeDescription-method Man page
[,Seqinfo-method Man page
seqlengths Man page
seqlengths<- Man page
seqlengths<-,ANY-method Man page
seqlengths,ANY-method Man page
seqlengths<-,Seqinfo-method Man page
seqlengths,Seqinfo-method Man page
seqlevels Man page
seqlevels<- Man page
seqlevels0 Man page
seqlevels<-,ANY-method Man page
seqlevels,ANY-method Man page
seqlevelsInGroup Man page
seqlevelsInUse Man page
seqlevelsInUse,CompressedList-method Man page
seqlevelsInUse,Vector-method Man page
seqlevels<-,Seqinfo-method Man page
seqlevels,Seqinfo-method Man page
seqlevelsStyle Man page
seqlevelsStyle<- Man page
seqlevelsStyle<-,ANY-method Man page
seqlevelsStyle,ANY-method Man page
seqlevelsStyle<-,character-method Man page
seqlevelsStyle,character-method Man page
seqlevels-wrappers Man page
seqnames Man page
seqnames<- Man page
seqnames,GenomeDescription-method Man page
seqnames<-,Seqinfo-method Man page
seqnames,Seqinfo-method Man page
show,GenomeDescription-method Man page
show,Seqinfo-method Man page
sortSeqlevels Man page
sortSeqlevels,ANY-method Man page
sortSeqlevels,character-method Man page
specData Man page
species Man page
species,GenomeDescription-method Man page
speciesMap Man page
summary.Seqinfo Man page
summary,Seqinfo-method Man page
validTaxIds Man page

Files

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

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