API for Bioconductor/GenomicFeatures
Tools for making and manipulating transcript centric annotations
| Global functions | |
|---|---|
| DEFAULT_CIRC_SEQS | Man page |
| Ensembl_fetchAttribTypeIdForTopLevelSequence | Source code |
| Ensembl_fetchChromLengthsFromCoreUrl | Source code |
| Ensembl_fetchTopLevelSequenceIds | Source code |
| Ensembl_getMySQLCoreDir | Source code |
| Ensembl_getMySQLCoreUrl | Source code |
| Ensembl_getTable | Source code |
| Ensembl_getTable_seq_region | Source code |
| Ensembl_listMySQLCoreDirs | Source code |
| FeatureDb | Man page Source code |
| FeatureDb-class | Man page |
| TXDB_column2table | Source code |
| TXDB_join_splicing_Rtables | Source code |
| TXDB_join_tables | Source code |
| TXDB_table_columns | Source code |
| TXDB_tables | Source code |
| TxDb | Man page Source code |
| TxDb-class | Man page |
| TxDb.genes | Source code |
| 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 |
| UCSC_dbselect | Source code |
| abbrevOrganismName | Source code |
| addMissingStrandCols | Source code |
| add_cds_cols | Source code |
| add_missing_exons | Source code |
| add_missing_transcripts | Source code |
| add_prefix_to_user_columns | Source code |
| add_tx_id_filter | Source code |
| adjustchromStarts | Source code |
| all_logical_NAs | Source code |
| as.list,TxDb-method | Man page |
| asBED,TxDb-method | Man page |
| asGFF,TxDb-method | Man page |
| as_db_columns | Source code |
| as_qualified | Source code |
| assert | Source code |
| assignMetadataList | Source code |
| break_in_parts | Source code |
| browseUCSCtrack | Man page Source code |
| build_SQL_CREATE_TABLE | 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 |
| build_SQL_FROM | Source code |
| build_SQL_FROM_splicing | Source code |
| build_SQL_SELECT | Source code |
| build_SQL_WHERE | Source code |
| capitalizeFirstLetter | 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 |
| checkAndRenamCols | Source code |
| checkTable | Source code |
| check_cds | Source code |
| check_colnames | Source code |
| check_exon_chrom | Source code |
| check_exon_rank | Source code |
| check_foreign_key | Source code |
| choosePrefix | Source code |
| class:FeatureDb | Man page |
| class:TxDb | Man page |
| collapse_df | Source code |
| columns | Source code |
| columns,TxDb-method | Man page |
| compareTxDbs | Source code |
| coordinate-mapping | Man page |
| coverageByTranscript | Man page Source code |
| dbEasyQuery | Source code |
| dbSchemaHasTxType | Source code |
| dbname2release | Source code |
| dbselect | Source code |
| debugSQL | Source code |
| detect_file_format | Source code |
| disjointExons | Man page |
| disjointExons,TxDb-method | Man page |
| distance,GenomicRanges,TxDb-method | Man page |
| eltNROWS | Source code |
| encodeSortedTableKey | Source code |
| 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 |
| exons_by_txids | Source code |
| exons_with_3utr | Source code |
| exons_with_5utr | Source code |
| extractByGeneID | Source code |
| extractCdsLocsFromUCSCTxTable | Source code |
| extractDataCols | Source code |
| extractFeaturesAsGRanges | Source code |
| extractFromTxDb | Source code |
| extractSplicingsFromUCSCTxTable | Source code |
| extractTranscriptSeqs | Man page |
| extractTranscriptSeqs,ANY-method | Man page |
| extractTranscriptSeqs,DNAString-method | Man page |
| extractTranscriptSeqsFromOneSeq | Source code |
| extractTranscriptSeqs_default | Source code |
| extractTranscriptsFromUCSCTxTable | Source code |
| extractTxName2GeneIdMappingFromUCSCTxTable | Source code |
| extractUCSCCdsStartEnd | Source code |
| extractUpstreamSeqs | Man page |
| extractUpstreamSeqs,GRangesList-method | Man page |
| extractUpstreamSeqs,GenomicRanges-method | Man page |
| extractUpstreamSeqs,TxDb-method | Man page |
| extract_and_combine | Source code |
| extract_cds_ranges_from_C1 | Source code |
| extract_cds_ranges_from_C2 | Source code |
| extract_cds_ranges_from_bm_result | Source code |
| extract_chrominfo_from_GRanges | Source code |
| extract_chromlengths_from_seq_region | Source code |
| extract_exons_from_GRanges | Source code |
| extract_features | Source code |
| extract_features_as_GRanges | Source code |
| extract_features_by | Source code |
| extract_features_by_gene | Source code |
| extract_genes_from_gff3_GRanges | Source code |
| extract_genes_from_gtf_GRanges | Source code |
| extract_numeric_attrib | Source code |
| extract_rank_from_id | Source code |
| extract_transcripts_from_GRanges | Source code |
| fast_XStringSet_unlist | Source code |
| features | Man page |
| features,FeatureDb-method | Man page |
| fetchChromLengthsFromEnsembl | Source code |
| fetchTxName2GeneIdMappingFromUCSC | Source code |
| fetch_Ensembl_chrominfo | Source code |
| fetch_Ensembl_splicings | Source code |
| fetch_Ensembl_transcripts | Source code |
| fetch_Ensembl_translations | Source code |
| fetch_UCSC_table | Source code |
| fetch_UCSC_txtable | Source code |
| findCompatibleMarts | Source code |
| find_available_attrib_groups | Source code |
| find_available_attrib_groups_for_each_dataset | Source code |
| find_exon_cds | Source code |
| fiveUTRsByTranscript | Man page |
| fiveUTRsByTranscript,TxDb-method | Man page |
| flush_rejected_tx_envir | Source code |
| format_chrominfo | Source code |
| format_genes | Source code |
| format_splicings | Source code |
| format_transcripts | Source code |
| format_txdb_dump | Source code |
| ftp_url_to_Ensembl_gtf | Source code |
| ftp_url_to_Ensembl_mysql | Source code |
| gather_Ensembl_metadata | Source code |
| generate_BioMart_data_anomaly_report | Source code |
| genes | Man page |
| genes,TxDb-method | Man page |
| genome2txcoords | Source code |
| getBM2 | Source code |
| getBiomartDbVersion | Source code |
| getChromInfoFromBiomart | Man page Source code |
| getChromInfoFromUCSC | Man page Source code |
| getMaintainer | Source code |
| getMetaDataValue | Source code |
| getPromoterSeq | Man page |
| getPromoterSeq,GRanges-method | Man page |
| getPromoterSeq,GRangesList-method | Man page |
| getSimpleTableNames | Source code |
| getSplicingsForTranscriptsWithCDSs | Source code |
| getTableColMapping | Source code |
| getTableNames | Source code |
| getTxDbVersion | Source code |
| get_Dbxref | Source code |
| get_EnsemblGenomes_kingdom_from_biomart | Source code |
| get_Ensembl_release_from_db_version | Source code |
| get_ID | Source code |
| get_Name | Source code |
| get_Parent | Source code |
| get_TxDb_seqinfo | Source code |
| get_TxDb_seqinfo0 | Source code |
| get_attribs_for_each_dataset | Source code |
| get_cds_IDX | Source code |
| get_cds_with_gene_parent_IDX | Source code |
| get_cds_with_noextx_parent_IDX | Source code |
| get_exon_IDX | Source code |
| get_exon_with_gene_parent_IDX | Source code |
| get_geneID | Source code |
| get_gene_IDX | Source code |
| get_gene_as_tx_IDX | Source code |
| get_gene_id | Source code |
| get_noextx_IDX | Source code |
| get_organism_from_Ensembl_Mart_dataset | Source code |
| get_phase | Source code |
| get_rejected_transcripts | Source code |
| get_stop_codon_IDX | Source code |
| get_toplevel_seq_region_ids | Source code |
| get_transcript_id | Source code |
| get_tx_IDX | Source code |
| get_type | Source code |
| graceful_as_integer | Source code |
| has_cds | Source code |
| has_col | Source code |
| has_utr | Source code |
| howToGetTxName2GeneIdMapping | Source code |
| id2name | Man page Source code |
| insert_data_into_table | 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 |
| isGoodTrack | Source code |
| joinDataFrameWithName2Val | Source code |
| join_genes_and_Rdf | Source code |
| keep_user_seqlevels_from_TxDb | Source code |
| keys | Source code |
| keys,TxDb-method | Man page |
| keysDispatch | Source code |
| keytypes,TxDb-method | Man page |
| light_txdb_dump | Source code |
| listCumsumShifted | Source code |
| listNames | Source code |
| load_chrominfo | Source code |
| load_genes | Source code |
| load_splicings | Source code |
| load_transcripts | Source code |
| lookup_dbname | Source code |
| lookup_organism_by_UCSC_genome | Source code |
| ls_ftp_url | Source code |
| ls_rejected_tx_envir | Source code |
| make3UTRsByTranscript | Source code |
| make5UTRsByTranscript | Source code |
| makeActiveChrList | Source code |
| makeAsList | Source code |
| makeBiomartChrominfo | Source code |
| makeBiomartGenes | Source code |
| makeBiomartSplicings | Source code |
| makeBiomartTranscripts | Source code |
| makeColAbbreviations | Source code |
| makeExonRankCol | Source code |
| makeFDbPackageFromUCSC | Man page Source code |
| makeFeatureDb | Source code |
| makeFeatureDbFromUCSC | Man page Source code |
| makeFeatureIds | Source code |
| makeIdsForUniqueDataFrameRows | Source code |
| makeJoinSQL | Source code |
| makeKeyList | Source code |
| makeMetadataList | Source code |
| makeObjectName | Source code |
| makePackageName | Man page Source code |
| makeSelectList | Source code |
| makeTableKey | Source code |
| makeToyTxDb | 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 |
| makeTxDbFromUCSCTxTable | Source code |
| makeTxDbPackage | Man page Source code |
| makeTxDbPackageFromBiomart | Man page Source code |
| makeTxDbPackageFromUCSC | Man page Source code |
| makeTxDb_normarg_chrominfo | Source code |
| makeTxDb_normarg_genes | Source code |
| makeTxDb_normarg_splicings | Source code |
| makeTxDb_normarg_transcripts | Source code |
| makeUCSCChrominfo | Source code |
| makeUCSCGenes | Source code |
| makeUTRsByTranscript | Source code |
| makeWhiteList | Source code |
| makeZeroRowDataFrame | Source code |
| make_DataFrame_from_df_list | Source code |
| make_Seqinfo_from_chrominfo | Source code |
| make_cds_df_from_ranges | Source code |
| make_circ_flags_from_circ_seqs | Source code |
| make_feature_columns | Source code |
| make_splicings | Source code |
| make_splicings_internal_cds_id | Source code |
| make_splicings_internal_exon_id | Source code |
| make_transcripts_internal_tx_id | Source code |
| mapFromTranscripts | Man page Source code |
| 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 Source code |
| mapToTranscripts,ANY,TxDb-method | Man page |
| mapToTranscripts,GenomicRanges,GRangesList-method | Man page |
| mapToTranscripts,GenomicRanges,GenomicRanges-method | Man page |
| match_and_check | Source code |
| mergeMaintainer | Source code |
| merge_seqinfo_and_infer_missing_seqlengths | Source code |
| merge_transcript_parts | Source code |
| microRNAs | Man page Source code |
| microRNAs,TxDb-method | Man page |
| missingTableInterpolator | Source code |
| mk_isActiveSeqReplacementValue | Source code |
| nearest-methods | Man page |
| nfer_Name_from_ID | Source code |
| nfer_rank_from_position | Source code |
| nfer_seqlengths | Source code |
| nfer_transcripts_from_exons | Source code |
| no_id | Source code |
| normAuthor | Source code |
| normMaintainer | Source code |
| normargExonStartsOrEnds | Source code |
| normarg_filter | Source code |
| normarg_id_prefix | Source code |
| normarg_metadata | Source code |
| normarg_organism | Source code |
| orderElementsByTranscription | Source code |
| organism,TxDb-method | Man page |
| pasteNames | Source code |
| 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 |
| pmapFromTranscripts_ranges | Source code |
| pmapToTranscripts | Man page |
| pmapToTranscripts,GRangesList,GRangesList-method | Man page |
| pmapToTranscripts,GenomicRanges,GRangesList-method | Man page |
| pmapToTranscripts,GenomicRanges,GenomicRanges-method | Man page |
| pmap_recycle | Source code |
| prepareBiomartMetadata | Source code |
| prepareGFFMetadata | Source code |
| prepareUCSCFeatureMetadata | Source code |
| prepareUCSCMetadata | Source code |
| prepare_dropped_msg | Source code |
| project_GRangesList_on_transcripts | Source code |
| project_GRanges_on_transcripts | Source code |
| promoters | Man page |
| promoters,TxDb-method | Man page |
| queryAnnotationDb | Source code |
| rank.CompressedList | Source code |
| rank_name_type | Source code |
| recognizedBiomartAttribs | Source code |
| reject_transcripts | Source code |
| relist_col | Source code |
| renamColsHelper | Source code |
| rename_by_dbxrefTag | Source code |
| restrict_to_tx_attrib | Source code |
| reverseColAbbreviations | Source code |
| s.named | Source code |
| sActiveSeq | Source code |
| s_character_or_factor | Source code |
| s_gtf_format | Source code |
| scanMart | Source code |
| select | Source code |
| 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_TxDb_seqlevels | Source code |
| set_group_names | Source code |
| set_transcriptome_seqinfo | Source code |
| show,TxDb-method | Man page |
| species,TxDb-method | Man page |
| split_df_into_GRL | Source code |
| stop_on_BioMart_data_anomaly | Source code |
| sum_width | Source code |
| supportedMiRBaseBuildValues | Man page Source code |
| supportedUCSCFeatureDbTables | Man page Source code |
| supportedUCSCFeatureDbTracks | Man page Source code |
| supportedUCSCtables | Man page Source code |
| syncSeqlevel | Source code |
| tRNAs | Man page Source code |
| tRNAs,TxDb-method | Man page |
| tableJoinSelector | Source code |
| tablename2track | Source code |
| tables_in_joins | Source code |
| test | Source code |
| test_makeTxDbFromGRanges_on_Ensembl_gtf | Source code |
| test_makeTxDbFromGRanges_on_Ensembl_organism_gtf | Source code |
| threeUTRsByTranscript | Man page |
| threeUTRsByTranscript,TxDb-method | Man page |
| tidyExons | Man page Source code |
| tidyIntrons | Man page Source code |
| tidyTranscripts | Man page Source code |
| tidy_seqinfo | 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 |
| translateChromsForBiomaRt | Source code |
| translateChromsForUCSC | Source code |
| translateCols | Source code |
| translateIds | Source code |
| unlist_strand | Source code |
| useMart2 | 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 |
| warning_on_BioMart_data_anomaly | Source code |
| warning_on_BioMart_utr_anomaly | Source code |
| writeGenericFeatureTable | Source code |
| writeMetadataFeatureTable | Source code |
| write_cds | Source code |
| write_chrominfo_table | Source code |
| write_exons | Source code |
| write_feature_table | Source code |
| write_gene_table | Source code |
| write_metadata_table | Source code |
| write_splicing_table | Source code |
| write_transcripts | Source code |
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