jmacdon/GenomicFeatures
Conveniently import and query gene models

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jmacdon/GenomicFeatures: Conveniently import and query gene models
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API

API for jmacdon/GenomicFeatures
Conveniently import and query gene models

Global functions
.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
.TXDB_join_splicing_Rtables Source code
.TXDB_join_tables Source code
.TxDb.genes Source code
.a_sample_of_foreign_transcripts_as_one_string 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_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
.capitalizeFirstLetter Source code
.checkAndRenamCols Source code
.check_cds Source code
.check_exon_chrom Source code
.check_exon_rank Source code
.check_foreign_key Source code
.choosePrefix Source code
.collapse_df Source code
.collect_parent_types Source code
.columns Source code
.dbSchemaHasTxType Source code
.dbname2release Source code
.dbselect Source code
.decorate_drop_msg Source code
.detect_file_format Source code
.drop_ID_prefix 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_UCSC_cds_start_end Source code
.extract_and_combine Source code
.extract_cds_locs_from_UCSC_txtable 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_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_mcols0 Source code
.extract_numeric_attrib Source code
.extract_rank_from_id Source code
.extract_splicings_from_UCSC_txtable Source code
.extract_transcripts_from_GRanges Source code
.extract_transcripts_from_UCSC_txtable Source code
.extract_txname2geneid_from_UCSC_txtable Source code
.fast_XStringSet_unlist 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
.fetch_attrib_type_id Source code
.fetch_txname2geneid_from_UCSC Source code
.find_available_attrib_groups Source code
.find_available_attrib_groups_for_each_dataset Source code
.find_exon_cds Source code
.flush_rejected_tx_envir Source code
.foreign_transcripts_stop_msg Source code
.foreign_transcripts_warning_msg Source code
.format_chrominfo Source code
.format_genes Source code
.format_splicings Source code
.format_transcripts Source code
.format_txdb_dump Source code
.gather_Ensembl_metadata Source code
.generate_BioMart_data_anomaly_report Source code
.genome2txcoords Source code
.getBM2 Source code
.getBiomartDbVersion Source code
.getMaintainer Source code
.getMetaDataValue Source code
.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_GENCODE_tx_tables Source code
.get_ID Source code
.get_Name Source code
.get_Parent Source code
.get_TxDb_seqinfo 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_gene_ids Source code
.get_noextx_IDX Source code
.get_phase Source code
.get_rejected_transcripts Source code
.get_stop_codon_IDX Source code
.get_supported_tx_tables Source code
.get_toplevel_seq_region_ids Source code
.get_transcript_id Source code
.get_tx_IDX Source code
.get_txname2geneid_mapdef Source code
.get_type Source code
.graceful_as_integer Source code
.has_cds Source code
.has_utr Source code
.infer_chrominfo_from_transcripts_and_splicings Source code
.infer_rank_from_position Source code
.infer_seqlengths Source code
.infer_transcripts_from_exons Source code
.is.named Source code
.isActiveSeq Source code
.is_character_or_factor Source code
.is_gtf_format Source code
.join_genes_and_Rdf Source code
.keys Source code
.keysDispatch Source code
.light_txdb_dump Source code
.listCumsumShifted Source code
.listNames Source code
.lookup_dbname 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
.makeJoinSQL Source code
.makeKeyList Source code
.makeMetadataList Source code
.makeObjectName Source code
.makeSelectList Source code
.makeTableKey Source code
.makeTxDb_normarg_chrominfo Source code
.makeTxDb_normarg_genes Source code
.makeTxDb_normarg_splicings Source code
.makeTxDb_normarg_transcripts Source code
.makeUTRsByTranscript Source code
.make_DataFrame_from_df_list Source code
.make_Seqinfo_from_chrominfo Source code
.make_TxDb_from_UCSC_txtable Source code
.make_UCSC_chrominfo Source code
.make_UCSC_genes Source code
.make_cds_df_from_ranges 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 Source code
.mapToTranscripts Source code
.match_and_check Source code
.mergeMaintainer Source code
.merge_seqinfo_and_infer_missing_seqlengths Source code
.merge_transcript_parts Source code
.microRNAs Source code
.missingTableInterpolator Source code
.mk_isActiveSeqReplacementValue 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_new2old_and_check_new_seqinfo Source code
.normarg_organism Source code
.orderElementsByTranscription Source code
.pasteNames Source code
.pmapFromTranscripts_ranges Source code
.pmap_recycle Source code
.prepareBiomartMetadata Source code
.prepareGFFMetadata Source code
.prepareUCSCFeatureMetadata Source code
.prepare_UCSC_metadata Source code
.project_GRangesList_on_transcripts Source code
.project_GRanges_on_transcripts Source code
.rank.CompressedList Source code
.rank_in_group Source code
.rank_name_type 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
.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
.stop_on_BioMart_data_anomaly Source code
.sum_width Source code
.syncSeqlevel Source code
.tRNAs Source code
.tableJoinSelector Source code
.tablename2track Source code
.tables_in_joins Source code
.test Source code
.tidy_seqinfo Source code
.translateChromsForBiomaRt Source code
.translateChromsForUCSC 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
.warn_about_circularity_guess 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
Ensembl_listMySQLCoreDirs 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
UCSC_dbselect 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
cds Man page
cds,TxDb-method Man page
cdsBy Man page
cdsBy,TxDb-method Man page
cdsByOverlaps Man page
cdsByOverlaps,TxDb-method Man page
checkTable Source code
check_colnames Source code
class:FeatureDb Man page
class:TxDb Man page
columns,TxDb-method Man page
compareTxDbs Source code
coordinate-mapping Man page
coverageByTranscript Man page Source code
dbEasyQuery Source code
debugSQL Source code
disjointExons Man page
disjointExons,TxDb-method Man page
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
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
extract_chromlengths_from_seq_region Source code
features Man page
features,FeatureDb-method Man page
fetchChromLengthsFromEnsembl Source code
findCompatibleMarts Source code
fiveUTRsByTranscript Man page
fiveUTRsByTranscript,TxDb-method Man page
ftp_url_to_Ensembl_gtf Source code
ftp_url_to_Ensembl_mysql 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
get_TxDb_seqinfo0 Source code
get_organism_from_Ensembl_Mart_dataset Source code
has_col 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
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
lookup_organism_by_UCSC_genome Source code
ls_ftp_url Source code
makeFDbPackageFromUCSC Man page Source code
makeFeatureDb Source code
makeFeatureDbFromUCSC Man page Source code
makeFeatureIds Source code
makeIdsForUniqueDataFrameRows Source code
makePackageName Man page 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
makeTxDbPackage Man page Source code
makeTxDbPackageFromBiomart Man page Source code
makeTxDbPackageFromUCSC Man page Source code
makeWhiteList Source code
makeZeroRowDataFrame Source code
make_exon_rank_col 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
map_SQLtypes_to_Rtypes Source code
microRNAs Man page
microRNAs,TxDb-method Man page
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
queryAnnotationDb Source code
recognizedBiomartAttribs Source code
scanMart 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_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
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
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
translateIds Source code
jmacdon/GenomicFeatures documentation built on Jan. 2, 2022, 7:40 a.m.

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