| 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 |
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
|
| tidy_exons |
Source code
|
| tidy_introns |
Source code
|
| tidy_seqinfo |
Source code
|
| tidy_transcripts |
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
|
