Bioconductor/GenomicFeatures
Query the gene models of a given organism/assembly

Package index
Search the Bioconductor/GenomicFeatures package
Vignettes
Functions
311
Source code
46
Man pages
31
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Bioconductor/GenomicFeatures: Query the gene models of a given organism/assembly
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API

API for Bioconductor/GenomicFeatures
Query the gene models of a given organism/assembly

Global functions
.GRangesList_getPromoterSeq Source code
.GRanges_getPromoterSeq Source code
.TXDB_join_splicing_Rtables Source code
.TXDB_join_tables Source code
.TxDb.genes Source code
.add_prefix_to_user_columns Source code
.as_db_columns Source code
.as_qualified Source code
.assert Source code
.assignMetadataList Source code
.break_in_parts Source code
.build_SQL_CREATE_TABLE Source code
.build_SQL_FROM Source code
.build_SQL_FROM_splicing Source code
.build_SQL_SELECT Source code
.build_SQL_WHERE Source code
.check_exon_chrom Source code
.check_exon_rank Source code
.check_supplied_tx_names Source code
.collapse_df Source code
.columns Source code
.dbSchemaHasTxType Source code
.default_proteinToGenome Source code
.eltNROWS Source code
.encodeSortedTableKey Source code
.exons_by_txids Source code
.exons_with_3utr Source code
.exons_with_5utr Source code
.extractByGeneID Source code
.extractDataCols Source code
.extractFeaturesAsGRanges Source code
.extractFromTxDb Source code
.extractTranscriptSeqsFromOneSeq Source code
.extractTranscriptSeqs_default Source code
.extract_and_combine Source code
.extract_cds_by_tx Source code
.extract_features Source code
.extract_features_as_GRanges Source code
.extract_features_by Source code
.extract_features_by_gene Source code
.fast_XStringSet_unlist Source code
.format_chrominfo Source code
.format_genes Source code
.format_splicings Source code
.format_transcripts Source code
.genome2txcoords Source code
.getSimpleTableNames Source code
.getSplicingsForTranscriptsWithCDSs Source code
.getTableColMapping Source code
.getTableNames Source code
.get_TxDb_seqinfo Source code
.infer_seqlengths Source code
.is.named Source code
.isActiveSeq Source code
.join_genes_and_Rdf Source code
.keys Source code
.keysDispatch Source code
.listCumsumShifted Source code
.make3UTRsByTranscript Source code
.make5UTRsByTranscript Source code
.makeActiveChrList Source code
.makeAsList Source code
.makeColAbbreviations Source code
.makeJoinSQL Source code
.makeKeyList Source code
.makeMetadataList Source code
.makeSelectList Source code
.makeTableKey Source code
.makeUTRsByTranscript Source code
.make_DataFrame_from_df_list Source code
.make_bad_names_msg Source code
.make_feature_columns Source code
.make_protein_ranges_from_cumwidths Source code
.mapFromTranscripts Source code
.mapToTranscripts Source code
.map_protein_to_cds Source code
.match_and_check Source code
.merge_seqinfo_and_infer_missing_seqlengths Source code
.missingTableInterpolator Source code
.mk_isActiveSeqReplacementValue Source code
.normargExonStartsOrEnds Source code
.normarg_new2old_and_check_new_seqinfo Source code
.orderElementsByTranscription Source code
.pmapFromTranscripts_ranges Source code
.pmap_recycle Source code
.project_GRangesList_on_transcripts Source code
.project_GRangesList_on_transcripts_BY_CHUNK Source code
.project_GRanges_on_transcripts Source code
.rank_in_group Source code
.relist_col Source code
.reverseColAbbreviations Source code
.select Source code
.set_TxDb_seqinfo Source code
.set_TxDb_seqlevels Source code
.set_group_names Source code
.set_transcriptome_seqinfo Source code
.split_df_into_GRL Source code
.sum_width Source code
.syncSeqlevel Source code
.tRNAs Source code
.tableJoinSelector Source code
.tables_in_joins Source code
.test Source code
.trim_first_and_last_ranges Source code
.unlist_strand Source code
.valid.FeatureDb Source code
.valid.TxDb Source code
.valid.cds.table Source code
.valid.chrominfo.table Source code
.valid.exon.table Source code
.valid.feature.table Source code
.valid.gene.table Source code
.valid.splicing.table Source code
.valid.transcript.table Source code
.validate.colnames Source code
FeatureDb Man page Source code
FeatureDb-class Man page
TXDB_column2table Source code
TXDB_table_columns Source code
TXDB_tables Source code
TxDb Man page Source code
TxDb-class Man page
TxDb_SELECT_from_INNER_JOIN Source code
TxDb_SELECT_from_chrominfo Source code
TxDb_SELECT_from_gene Source code
TxDb_SELECT_from_splicing_bundle Source code
TxDb_SELECT_from_splicings Source code
TxDb_SELECT_from_transcript Source code
TxDb_schema_version Source code
UCSCFeatureDbTableSchema Man page Source code
as.list,TxDb-method Man page
asBED,TxDb-method Man page
asGFF,TxDb-method Man page
browseUCSCtrack Man page Source code
build_SQL_CREATE_chrominfo_table Source code
build_SQL_CREATE_feature_table Source code
build_SQL_CREATE_gene_table Source code
build_SQL_CREATE_splicing_table Source code
call_fun_in_txdbmaker Source code
cds Man page
cds,TxDb-method Man page
cdsBy Man page
cdsBy,TxDb-method Man page
cdsByOverlaps Man page
cdsByOverlaps,TxDb-method Man page
class:FeatureDb Man page
class:TxDb Man page
columns,TxDb-method Man page
compareTxDbs Source code
coordinate-mapping Man page
coordinate-mapping-methods Man page
coverageByTranscript Man page Source code
dbEasyQuery Source code
debugSQL Source code
distance,GenomicRanges,TxDb-method Man page
exonicParts Man page Source code
exons Man page
exons,TxDb-method Man page
exonsBy Man page
exonsBy,TxDb-method Man page
exonsByOverlaps Man page
exonsByOverlaps,TxDb-method Man page
extendExonsIntoIntrons Man page Source code
extractTranscriptSeqs Man page
extractTranscriptSeqs,ANY-method Man page
extractTranscriptSeqs,DNAString-method Man page
extractUpstreamSeqs Man page
extractUpstreamSeqs,GRangesList-method Man page
extractUpstreamSeqs,GenomicRanges-method Man page
extractUpstreamSeqs,TxDb-method Man page
features Man page
features,FeatureDb-method Man page
fiveUTRsByTranscript Man page
fiveUTRsByTranscript,TxDb-method Man page
format_txdb_dump Source code
genes Man page
genes,TxDb-method Man page
getChromInfoFromBiomart Man page Source code
getPromoterSeq Man page
getPromoterSeq,GRanges-method Man page
getPromoterSeq,GRangesList-method Man page
getTerminatorSeq Man page
getTerminatorSeq,GRanges-method Man page
getTerminatorSeq,GRangesList-method Man page
get_TxDb_seqinfo0 Source code
has_col Source code
id2name Man page Source code
intronicParts Man page Source code
intronsByTranscript Man page
intronsByTranscript,TxDb-method Man page
isActiveSeq Man page
isActiveSeq,TxDb-method Man page
isActiveSeq<- Man page
isActiveSeq<-,TxDb-method Man page
keys,TxDb-method Man page
keytypes,TxDb-method Man page
load_chrominfo Source code
load_genes Source code
load_genome Source code
load_splicings Source code
load_transcripts Source code
makeFDbPackageFromUCSC Man page Source code
makeFeatureDbFromUCSC Man page Source code
makeIdsForUniqueDataFrameRows Source code
makePackageName Man page Source code
makeTxDb Man page Source code
makeTxDbFromBiomart Man page Source code
makeTxDbFromEnsembl Man page Source code
makeTxDbFromGFF Man page Source code
makeTxDbFromGRanges Man page Source code
makeTxDbFromUCSC Man page Source code
makeTxDbPackage Man page Source code
makeTxDbPackageFromBiomart Man page Source code
makeTxDbPackageFromUCSC Man page Source code
makeZeroRowDataFrame Source code
mapFromTranscripts Man page
mapFromTranscripts,GenomicRanges,GRangesList-method Man page
mapFromTranscripts,GenomicRanges,GenomicRanges-method Man page
mapIdsToRanges Man page
mapIdsToRanges,TxDb-method Man page
mapRangesToIds Man page
mapRangesToIds,TxDb-method Man page
mapToTranscripts Man page
mapToTranscripts,ANY,TxDb-method Man page
mapToTranscripts,GenomicRanges,GRangesList-method Man page
mapToTranscripts,GenomicRanges,GenomicRanges-method Man page
microRNAs Man page Source code
nearest-methods Man page
organism,TxDb-method Man page
pcoverageByTranscript Man page Source code
pmapFromTranscripts Man page
pmapFromTranscripts,GenomicRanges,GRangesList-method Man page
pmapFromTranscripts,GenomicRanges,GenomicRanges-method Man page
pmapFromTranscripts,IntegerRanges,GRangesList-method Man page
pmapFromTranscripts,IntegerRanges,GenomicRanges-method Man page
pmapToTranscripts Man page
pmapToTranscripts,GRangesList,GRangesList-method Man page
pmapToTranscripts,GenomicRanges,GRangesList-method Man page
pmapToTranscripts,GenomicRanges,GenomicRanges-method Man page
promoters Man page
promoters,TxDb-method Man page
proteinToGenome Man page
proteinToGenome,ANY-method Man page
proteinToGenome,GRangesList-method Man page
queryAnnotationDb Source code
saveRDS,TxDb-method Man page
select,TxDb-method Man page
select-methods Man page
seqinfo,TxDb-method Man page
seqlevels0,TxDb-method Man page
seqlevels<-,TxDb-method Man page
setDataFrameColClass Source code
set_user_seqlevels_and_genome Source code
show,TxDb-method Man page
supportedMiRBaseBuildValues Man page Source code
supportedUCSCFeatureDbTables Man page Source code
supportedUCSCFeatureDbTracks Man page Source code
supportedUCSCtables Man page Source code
tRNAs Man page
tRNAs,TxDb-method Man page
terminators Man page
terminators,TxDb-method Man page
threeUTRsByTranscript Man page
threeUTRsByTranscript,TxDb-method Man page
tidyExons Man page Source code
tidyIntrons Man page Source code
tidyTranscripts Man page Source code
transcriptLengths Man page Source code
transcriptLocs2refLocs Man page Source code
transcriptWidths Man page Source code
transcripts Man page
transcripts,TxDb-method Man page
transcriptsBy Man page
transcriptsBy,TxDb-method Man page
transcriptsByOverlaps Man page
transcriptsByOverlaps,TxDb-method Man page
translateCols Source code
Bioconductor/GenomicFeatures documentation built on June 14, 2025, 5:43 p.m.

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