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

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

Global functions
..safe_match Source code
.Seqinfo.merge Source code
.Seqinfo.mergexy Source code
.add_NCBI_cols_to_Ensembl_chrom_info Source code
.add_NCBI_cols_to_UCSC_chrom_info Source code
.add_ensembl_column Source code
.attrib_type_codes_to_ids_from_Ensembl_FTP Source code
.check_assembly_summary Source code
.compactDataFrame Source code
.do_join Source code
.dropPrefix Source code
.external_db_names_to_ids_from_Ensembl_FTP Source code
.fetch_Ensembl_column Source code
.fetch_Ensembl_seqlevels_from_UCSC Source code
.fetch_assembly_report_from_url Source code
.fetch_attribs_from_Ensembl_FTP Source code
.fetch_species_index_from_url Source code
.fetch_synonyms_from_Ensembl_FTP Source code
.fetch_table_from_UCSC Source code
.fetch_ucsc2ensembl_from_chromAlias_table Source code
.fetch_ucscToEnsembl_table Source code
.find_NCBI_assembly_info_for_Ensembl_species_info Source code
.find_core_db_in_Ensembl_FTP_core_dbs Source code
.find_core_db_in_Ensembl_FTP_species_index Source code
.form_assembly_report_url Source code
.format_Ensembl_chrom_info Source code
.format_NCBI_chrom_info Source code
.from_DataFrame_to_Seqinfo Source code
.getDataInFile Source code
.getDatadir Source code
.getNamedFiles Source code
.getNbPart Source code
.getPostNbPart Source code
.get_Ensembl_FTP_species_index_url Source code
.get_Ensembl_FTP_top_url Source code
.get_Ensembl_linker Source code
.get_NCBI_chrom_info_from_accession Source code
.get_NCBI_linker Source code
.get_Seqinfo_seqlevelsStyle Source code
.get_chrom_info_for_registered_UCSC_genome Source code
.get_chrom_info_for_unregistered_UCSC_genome Source code
.get_chrom_info_from_Ensembl_FTP Source code
.get_genome_as_factor Source code
.get_seqlevelsStyle_for_NCBI_seqlevels Source code
.get_seqlevelsStyle_from_seqlevels_and_genome Source code
.guessSpeciesStyle Source code
.hasPrefix Source code
.isShortNb Source code
.isSupportedSeqnamesStyle Source code
.is_NCBI_assembly_or_UCSC_genome Source code
.is_RefSeq_accession Source code
.is_genbank_assembly_accession Source code
.is_refseq_assembly_accession Source code
.list_Ensembl_FTP_core_dbs Source code
.load_or_fetch_species_index_from_url Source code
.load_registered_NCBI_assemblies Source code
.load_registered_NCBI_assembly Source code
.lookup_NCBI_assembly2accession Source code
.lookup_abbrev_species_in_core_dbs Source code
.lookup_refseq_assembly_accession Source code
.lookup_species Source code
.make_Seqinfo_from_genome Source code
.make_assembly_accessions_table_from_assembly_summaries Source code
.make_extra_info_col Source code
.map_Ensembl_seqlevels_to_NCBI_seqlevels Source code
.map_NCBI_assembly_to_UCSC_genome Source code
.map_UCSC_genome_to_NCBI_assembly Source code
.map_UCSC_seqlevel_to_NCBI_seqlevel Source code
.map_UCSC_seqlevels_to_NCBI_seqlevels Source code
.match_Ensembl_synonmys_to_NCBI_col Source code
.match_UCSC_seqlevel_part2_to_NCBI_accn Source code
.match_UCSC_seqlevel_to_NCBI_accn Source code
.match_UCSC_seqlevels_part2_to_NCBI_accns Source code
.match_UCSC_seqlevels_to_NCBI_accns Source code
.mk_progress_str Source code
.normalize_organism Source code
.normarg_assembly_accession Source code
.normarg_genome Source code
.normarg_isCircular Source code
.normarg_seqlengths Source code
.normarg_seqlevels Source code
.normarg_seqlevelsStyle Source code
.onLoad Source code
.one_to_many_msg Source code
.parse_script_for_registered_UCSC_genome Source code
.predict_core_db_in_Ensembl_FTP_grch37 Source code
.replace_seqlevels_style Source code
.reverse_new2old Source code
.set_Seqinfo_seqlevelsStyle Source code
.set_seqlevelsStyle_from_seqlevels_and_genome Source code
.showOutputAsCharacter Source code
.simple_read_table Source code
.stop_on_ambiguous_lookup Source code
.supportedSeqlevelsStyles Source code
.supportedSeqnameMappings Source code
.test Source code
.try_to_fetch_ucsc2ensembl_from_chromAlias Source code
.try_to_fetch_ucscToEnsembl 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
DEFAULT_CIRC_SEQS Man page
GenomeDescription Man page Source code
GenomeDescription-class Man page
Seqinfo Man page Source code
Seqinfo-class Man page
[,Seqinfo-method Man page
as.data.frame,Seqinfo-method Man page
as.data.frame.Seqinfo Man page Source code
available.species Man page Source code
bsgenomeName Man page
bsgenomeName,GenomeDescription-method Man page
build_and_save_assembly_accessions_table Source code
checkCompatibleSeqinfo Man page Source code
check_species_info Source code
check_tax_id 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
compactPrintNamedAtomicVector Source code
dropSeqlevels Man page Source code
drop_cols Source code
extractSeqlevels Man page Source code
extractSeqlevelsByGroup Man page Source code
fetchExtendedChromInfoFromUCSC Man page Source code
fetch_ChromInfo_from_UCSC Source code
fetch_GenBankAccn2seqlevel_from_NCBI Source code
fetch_assembly_report Source code
fetch_assembly_summary Source code
fetch_chrom_sizes_from_UCSC Source code
fetch_default_coord_systems_from_Ensembl_FTP Source code
fetch_seq_regions_from_Ensembl_FTP Source code
fetch_species_index_from_Ensembl_FTP Source code
fetch_table_from_Ensembl_FTP Source code
fetch_table_from_UCSC Source code
fetch_table_from_url Source code
find_NCBI_assembly_info_for_accession 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
getChromInfoFromEnsembl Man page Source code
getChromInfoFromNCBI Man page Source code
getChromInfoFromUCSC Man page Source code
getDanglingSeqlevels Source code
getSeqlevelsReplacementMode Source code
get_Ensembl_FTP_core_db_url Source code
get_Ensembl_FTP_gtf_url Source code
get_Ensembl_FTP_mysql_url 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
is_primary_key Source code
is_single_value Source code
join_dfs Source code
keepSeqlevels Man page Source code
keepStandardChromosomes Man page Source code
length,Seqinfo-method Man page
listOrganisms Man page Source code
list_Ensembl_FTP_releases Source code
list_ftp_dir Source code
loadTaxonomyDb Man page Source code
lookup_organism_by_tax_id Source code
lookup_tax_id_by_organism Source code
makeNewSeqnames Source code
make_circ_flags_from_circ_seqs Source code
mapGenomeBuilds Man page Source code
mapSeqlevels Man page 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
normarg_new2old 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
registered_NCBI_assemblies Man page Source code
registered_UCSC_genomes 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
rename_cols Source code
restoreSeqlevels Man page 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,Seqinfo-method Man page
seqlevelsStyle,character-method Man page
seqlevelsStyle<- Man page
seqlevelsStyle<-,ANY-method Man page
seqlevelsStyle<-,Seqinfo-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
solid_match Source code
solid_match2 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
stop_if_not_primary_key Source code
summary,Seqinfo-method Man page
summary.Seqinfo Man page Source code
use_species_index_from_Ensembl_FTP Source code
GenomeInfoDb documentation built on April 9, 2021, 6 p.m.

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