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

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317
Source code
172
Man pages
13
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Bioconductor/GenomeInfoDb: Utilities for manipulating chromosome names, including modifying them to follow a particular naming style
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API for Bioconductor/GenomeInfoDb
Utilities for manipulating chromosome names, including modifying them to follow a particular naming style

Global functions
.add_NCBI_cols_to_Ensembl_chrom_info Source code
.add_NCBI_cols_to_UCSC_chrom_info Source code
.add_ensembl_column Source code
.assembly_not_found_msg Source code
.attrib_type_codes_to_ids_from_Ensembl_FTP Source code
.check_assembly_summary Source code
.check_chrom_sizes Source code
.clean_file Source code
.compactDataFrame Source code
.do_join Source code
.dropPrefix Source code
.external_db_names_to_ids_from_Ensembl_FTP Source code
.extract_species_info_from_species_index Source code
.fetch_Ensembl_column Source code
.fetch_assembly_report_from_url Source code
.fetch_attribs_from_Ensembl_FTP Source code
.fetch_chrom_sizes_from_UCSC_bigZips Source code
.fetch_chrom_sizes_from_UCSC_database Source code
.fetch_raw_chrom_info_from_UCSC Source code
.fetch_species_index_from_url Source code
.fetch_synonyms_from_Ensembl_FTP 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
.ftp_listing_as_matrix 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_raw_chrom_info_for_registered_UCSC_genome 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
.list_Ensembl_FTP_releases Source code
.list_ftp_dir Source code
.load_or_fetch_species_index_from_url Source code
.load_registered_NCBI_assemblies Source code
.load_registered_NCBI_assembly Source code
.load_stored_amol_info_for_UCSC_genome Source code
.lookup_NCBI_assembly2accession Source code
.lookup_refseq_assembly_accession Source code
.lookup_species_in_core_dbs Source code
.lookup_species_in_species_index Source code
.make_Seqinfo_from_UCSC_chrominfo Source code
.make_Seqinfo_from_genome Source code
.make_assembly_accessions_table_from_assembly_summaries Source code
.make_extra_info_col Source code
.make_matrix_data_from_list Source code
.make_species_info_for_grch37 Source code
.map_Ensembl_seqlevels_to_NCBI_seqlevels Source code
.map_NCBI_assembly_to_UCSC_genome Source code
.map_NCBI_or_RefSeq_seqlevels_to_UCSC Source code
.map_NCBI_or_RefSeq_seqlevels_to_hg38 Source code
.map_UCSC_genome_to_NCBI_assembly Source code
.map_UCSC_seqlevels_to_NCBI_or_RefSeq Source code
.map_UCSC_seqlevels_to_NCBI_seqlevels Source code
.map_hg38_seqlevels_to_NCBI_or_RefSeq Source code
.match_Ensembl_synonmys_to_NCBI_col Source code
.match_UCSC_seqlevels_part2_to_NCBI_accns Source code
.match_UCSC_seqlevels_to_NCBI_accns Source code
.merge_Seqinfo_objects Source code
.merge_two_Seqinfo_objects Source code
.mk_progress_str Source code
.norm_GenomeDescription_arg Source code
.normalize_organism Source code
.normalize_species Source code
.normarg_assembly_accession Source code
.normarg_ftp_dir 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
.please_install_missing_CRAN_pkgs 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
.stop_on_ambiguous_lookup Source code
.supportedSeqlevelsStyles Source code
.supportedSeqnameMappings Source code
.table_can_contain_CRs Source code
.test Source code
.try_to_fetch_ucsc2ensembl_from_chromAlias Source code
.try_to_fetch_ucscToEnsembl Source code
.update_Seqinfo 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
.warn_about_circularity_guess Source code
.warn_species_was_ignored Source code
DEFAULT_CIRC_SEQS Man page
GenomeDescription Man page Source code
GenomeDescription-class Man page
NCBI-utils Man page
OLD_fetch_table_dump_from_Ensembl_FTP Source code
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
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
fetch_assembly_report Man page 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_dump_from_Ensembl_FTP Source code
fetch_table_dump_from_UCSC Source code
fetch_table_from_url Source code
find_NCBI_assembly_ftp_dir Man page 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
get_and_fix_chrom_info_from_UCSC Man page Source code
get_current_Ensembl_release 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_ftp_dir Man page 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
merge.Seqinfo Man page Source code
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
read_UCSC_assembled_molecules_db_table Source code
registered_NCBI_assemblies Man page Source code
registered_UCSC_genomes Man page Source code
releaseDate Man page
releaseDate,GenomeDescription-method Man page
renameSeqlevels Man page Source code
rename_cols Source code
restoreSeqlevels Man page Source code
saveAssembledMoleculesInfoFromUCSC 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
simple_read_table 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
stop_if_not_primary_key Source code
summary,Seqinfo-method Man page
summary.Seqinfo Man page Source code
update,Seqinfo-method Man page
update.Seqinfo Man page Source code
use_species_index_from_Ensembl_FTP Source code
Bioconductor/GenomeInfoDb documentation built on April 19, 2024, 9:28 a.m.

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