GenomeInfoDb: Utilities for manipulating chromosome and other 'seqname' identifiers
Version 1.12.0

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.

Browse man pages Browse package API and functions Browse package files

AuthorSonali Arora, Martin Morgan, Marc Carlson, H. Pagès
Bioconductor views Annotation DataRepresentation Genetics GenomeAnnotation
Date of publicationNone
MaintainerBioconductor Package Maintainer <maintainer@bioconductor.org>
LicenseArtistic-2.0
Version1.12.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("GenomeInfoDb")

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

Functions

GenomeDescription Man page Source code
GenomeDescription-class Man page
Seqinfo Man page Man page Source code
Seqinfo-class Man page
Seqinfo.merge Source code
Seqinfo.mergexy Source code
[,Seqinfo-method Man page
as.data.frame,Seqinfo-method Man page
available.species Man page Source code
bsgenomeName Man page
bsgenomeName,GenomeDescription-method Man page
build_and_save_assembly_accessions_table Source code
checkForAValidTaxonomyId Source code
check_assembly_summary Source code
class:GenomeDescription Man page
class:Seqinfo Man page
coerce,DataFrame,Seqinfo-method Man page
coerce,data.frame,Seqinfo-method Man page
commonName Man page
commonName,GenomeDescription-method Man page
compactDataFrame Source code
compactPrintNamedAtomicVector Source code
dropPrefix Source code
dropSeqlevels Man page Source code
extractSeqlevels Man page Source code
extractSeqlevelsByGroup Man page Source code
fetchExtendedChromInfoFromUCSC Man page Source code
fetchSequenceInfo Source code
fetch_ChromInfo_from_UCSC Source code
fetch_GenBankAccn2seqlevel_from_NCBI Source code
fetch_assembly_report Source code
fetch_assembly_report_from_URL Source code
fetch_assembly_summary Source code
fetch_sequence_info_for_UCSC_genome Source code
genome Man page
genome,ANY-method Man page
genome,Seqinfo-method Man page
genome<- Man page
genome<-,ANY-method Man page
genome<-,Seqinfo-method Man page
genomeBuilds Man page Source code
genomeStyles Man page Source code
getDanglingSeqlevels Source code
getDataInFile Source code
getDatadir Source code
getNamedFiles Source code
getNbPart Source code
getPostNbPart Source code
getSeqlevelsReplacementMode Source code
getTaxonomyId Source code
guessSpeciesStyle Source code
hasPrefix Source code
intersect,Seqinfo,Seqinfo-method Man page
isCircular Man page
isCircular,ANY-method Man page
isCircular,Seqinfo-method Man page
isCircular<- Man page
isCircular<-,ANY-method Man page
isCircular<-,Seqinfo-method Man page
isRoman Source code
keepSeqlevels Man page Source code
keepStandardChromosomes Man page Source code
length,Seqinfo-method Man page
listOrganisms Man page Source code
list_ftp_dir Source code
lookupSpeciesFromTaxId Source code
lookup_refseq_assembly_accession Source code
makeNewSeqnames Source code
makeSeqinfoFromDataFrame Source code
make_assembly_accessions_table_from_assembly_summaries Source code
make_assembly_report_URL Source code
mapGenomeBuilds Man page Source code
mapSeqlevels Man page Source code
map_UCSC_seqlevel_to_NCBI_seqlevel Source code
match_UCSC_seqlevel_part2_to_NCBI_accn Source code
match_UCSC_seqlevel_to_NCBI_accn Source code
merge,NULL,Seqinfo-method Man page
merge,Seqinfo,NULL-method Man page
merge,Seqinfo,Seqinfo-method Man page
merge,Seqinfo,missing-method Man page
merge,missing,Seqinfo-method Man page
mergeNamedAtomicVectors Source code
names,Seqinfo-method Man page
names<-,Seqinfo-method Man page
normalize_organism Source code
normargGenome Source code
normargIsCircular Source code
normargSeqlengths Source code
normargSeqlevels Source code
normarg_assembly_accession Source code
orderSeqlevels Man page Source code
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 Source code
releaseDate Man page
releaseDate,GenomeDescription-method Man page
releaseName Man page
releaseName,GenomeDescription-method Man page
renameSeqlevels Man page Source code
replace_seqlevels_style Source code
restoreSeqlevels Man page Source code
reverseNew2old Source code
sShortNb Source code
sSupportedSeqnamesStyle Source code
sTRUEorFALSE Source code
s_genbank_assembly_accession Source code
s_refseq_assembly_accession Source code
safe_match Source code
seqinfo Man page
seqinfo,GenomeDescription-method Man page
seqinfo<- Man page
seqlengths Man page
seqlengths,ANY-method Man page
seqlengths,Seqinfo-method Man page
seqlengths<- Man page
seqlengths<-,ANY-method Man page
seqlengths<-,Seqinfo-method Man page
seqlevels Man page
seqlevels,ANY-method Man page
seqlevels,Seqinfo-method Man page
seqlevels-wrappers Man page
seqlevels0 Man page
seqlevels<- Man page
seqlevels<-,ANY-method Man page
seqlevels<-,Seqinfo-method Man page
seqlevelsInGroup Man page Source code
seqlevelsInUse Man page
seqlevelsInUse,CompressedList-method Man page
seqlevelsInUse,Vector-method Man page
seqlevelsStyle Man page
seqlevelsStyle,ANY-method Man page
seqlevelsStyle,character-method Man page
seqlevelsStyle<- Man page
seqlevelsStyle<-,ANY-method Man page
seqlevelsStyle<-,character-method Man page
seqnames Man page
seqnames,GenomeDescription-method Man page
seqnames,Seqinfo-method Man page
seqnames<- Man page
seqnames<-,Seqinfo-method Man page
sequenceGeometryHasChanged Source code
show,GenomeDescription-method Man page
show,Seqinfo-method Man page
showCompactDataFrame Source code
showGenomeDescription Source code
showOutputAsCharacter Source code
sortSeqlevels Man page
sortSeqlevels,ANY-method Man page
sortSeqlevels,character-method Man page
species Man page
species,GenomeDescription-method Man page
standardChromosomes Man page Source code
standard_fetch_extended_ChromInfo_from_UCSC Source code
summary,Seqinfo-method Man page
summary.Seqinfo Man page Source code
supportedSeqlevelsStyles Source code
supportedSeqnameMappings Source code
taxonomyId Source code
test Source code
valid.Seqinfo Source code
valid.Seqinfo.genome Source code
valid.Seqinfo.isCircular Source code
valid.Seqinfo.seqlengths Source code
valid.Seqinfo.seqnames Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/GenomeDescription-class.R
R/Seqinfo-class.R
R/assembly-utils.R
R/available.species.R
R/fetchExtendedChromInfoFromUCSC.R
R/fetchSequenceInfo.R
R/mapGenomeBuilds.R
R/rankSeqlevels.R
R/seqinfo.R
R/seqlevels-wrappers.R
R/seqlevelsStyle.R
R/utils.R
R/zzz.R
build
build/vignette.rds
inst
inst/doc
inst/doc/Accept-organism-for-GenomeInfoDb.R
inst/doc/Accept-organism-for-GenomeInfoDb.Rnw
inst/doc/Accept-organism-for-GenomeInfoDb.pdf
inst/doc/GenomeInfoDb.R
inst/doc/GenomeInfoDb.Rnw
inst/doc/GenomeInfoDb.pdf
inst/extdata
inst/extdata/assembly_accessions.rda
inst/extdata/dataFiles
inst/extdata/dataFiles/Arabidopsis_thaliana.txt
inst/extdata/dataFiles/Caenorhabditis_elegans.txt
inst/extdata/dataFiles/Canis_familiaris.txt
inst/extdata/dataFiles/Cyanidioschyzon_merolae.txt
inst/extdata/dataFiles/Drosophila_melanogaster.txt
inst/extdata/dataFiles/Homo_sapiens.txt
inst/extdata/dataFiles/Mus_musculus.txt
inst/extdata/dataFiles/Oryza_sativa.txt
inst/extdata/dataFiles/Populus_trichocarpa.txt
inst/extdata/dataFiles/Rattus_norvegicus.txt
inst/extdata/dataFiles/Saccharomyces_cerevisiae.txt
inst/extdata/dataFiles/Zea_mays.txt
inst/extdata/dataFiles/genomeMappingTbl.csv
inst/unitTests
inst/unitTests/test_Seqinfo-class.R
inst/unitTests/test_mapGenomeBuilds.R
inst/unitTests/test_seqlevels-wrappers.R
inst/unitTests/test_seqlevelsStyle.R
inst/unitTests/test_utils.R
man
man/GenomeDescription-class.Rd
man/Seqinfo-class.Rd
man/available.species.Rd
man/fetchExtendedChromInfoFromUCSC.Rd
man/mapGenomeBuilds.Rd
man/rankSeqlevels.Rd
man/seqinfo.Rd
man/seqlevels-wrappers.Rd
man/seqlevelsStyle.Rd
tests
tests/run_unitTests.R
vignettes
vignettes/Accept-organism-for-GenomeInfoDb.Rnw
vignettes/GenomeInfoDb.Rnw
GenomeInfoDb documentation built on May 20, 2017, 10:12 p.m.