FelixErnst/EpiTxDb
Storing and accessing epitranscriptomic information using the AnnotationDbi interface

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Search the FelixErnst/EpiTxDb package
Vignettes
Functions
201
Source code
24
Man pages
13
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FelixErnst/EpiTxDb: Storing and accessing epitranscriptomic information using the AnnotationDbi interface
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API

API for FelixErnst/EpiTxDb
Storing and accessing epitranscriptomic information using the AnnotationDbi interface

Global functions
.EPITXDB_add_table_bundle Source code
.EPITXDB_join_tables Source code
.EpiTxDb Man page
.add_reference_information_tRNAdb Source code
.add_sequence_check_to_metadata Source code
.add_tRNAdb_metadata_columns Source code
.as_db_columns Source code
.build_SQL_CREATE_TABLE Source code
.check_RMBase_files_available Source code
.check_tx_sequences Source code
.columns Source code
.compareFUN_GENOME_TO_TX Source code
.compareFUN_GENOME_TO_TX_List Source code
.compareFUN_TX_TO_GENOME Source code
.compareFUN_TX_TO_GENOME_List Source code
.download_RMBase_files Source code
.encodeSortedTableKey Source code
.extractFromEpiTxDb Source code
.extract_GRanges_from_RMBase Source code
.extract_features_by Source code
.extract_modifications Source code
.extract_modifications_as_GRanges Source code
.fix_non_standard_mod_types Source code
.fixed_queryHits Source code
.fixed_subjectHits Source code
.format_feature_columns Source code
.format_modifications Source code
.format_reactions Source code
.format_references Source code
.format_seqnames Source code
.format_specifiers Source code
.format_txdb_dump Source code
.gene_names_to_chromosome Source code
.getSimpleTableNames Source code
.getTableColMapping Source code
.getTableNames Source code
.get_EpiTxDb_seqinfo Source code
.get_EpiTxDb_seqlevels Source code
.get_RMBase_colnames Source code
.get_RMBase_data Source code
.get_RMBase_files Source code
.get_RMBase_files_available Source code
.get_RMBase_genomes Source code
.get_RMBase_header Source code
.get_RMBase_mod Source code
.get_RMBase_rnames Source code
.get_gr_modifications Source code
.get_gr_reactions Source code
.get_gr_references Source code
.get_gr_specifiers Source code
.get_seqnames Source code
.get_strand_u_GRangesList Source code
.hitsFUN_GENOME_TO_TX Source code
.hitsFUN_TX_TO_GENOME Source code
.keys Source code
.keysDispatch Source code
.listAvailableGenomesFromRMBase Source code
.makeColAbbreviations Source code
.makeEpiTxDb_normarg_metadata Source code
.makeEpiTxDb_normarg_modifications Source code
.makeEpiTxDb_normarg_reactions Source code
.makeEpiTxDb_normarg_references Source code
.makeEpiTxDb_normarg_specifiers Source code
.makeJoinSQL Source code
.makeKeyList Source code
.makeSelectList Source code
.makeTableKey Source code
.make_ids Source code
.make_modifications_internal_mod_id Source code
.make_reactions_ids Source code
.make_references_ids Source code
.make_specifiers_ids Source code
.map_modifications_to_sequences Source code
.non_hits Source code
.norm_tx Source code
.normarg_scale Source code
.read_RMBase_file Source code
.remove_incompatible_mod_by_seq Source code
.resultFUN_GENOME_TO_TX Source code
.resultFUN_GENOME_TO_TX_List Source code
.resultFUN_TX_TO_GENOME Source code
.resultFUN_TX_TO_GENOME_List Source code
.reverseColAbbreviations Source code
.select Source code
.seqs_l_by Source code
.seqs_rl_by Source code
.seqs_rl_strand Source code
.shift Source code
.shrink_df Source code
.simplify_chromosome_identifiers Source code
.split_into_GRL Source code
.tableJoinSelector Source code
.valid.EpiTxDb Source code
.valid.modification.table Source code
.valid.reaction.table Source code
.valid.reference.table Source code
.valid.seqnames.table Source code
.valid.specifier.table Source code
.write_metadata_table Source code
.write_modification2reaction_table Source code
.write_modification2reference_table Source code
.write_modification2specifier_table Source code
.write_modification_table Source code
.write_reaction_table Source code
.write_reference_table Source code
.write_seqnames_table Source code
.write_specifier_table Source code
.zoom0 Source code
EPITXDB_RMBASE_URL Man page
EPITXDB_column2table Source code
EPITXDB_table2joinColumns Source code
EPITXDB_table_columns Source code
EPITXDB_tables Source code
EpiTxDb Man page Source code
EpiTxDb-class Man page
EpiTxDb-data Man page
EpiTxDb-package Man page
EpiTxDb-package#' Man page
EpiTxDb_SELECT_from_LEFT_JOIN Source code
EpiTxDb_SELECT_from_modification Source code
EpiTxDb_SELECT_from_reaction Source code
EpiTxDb_SELECT_from_reference Source code
EpiTxDb_SELECT_from_seqnames Source code
EpiTxDb_SELECT_from_specifier Source code
EpiTxDb_schema_version Source code
as.integer,Ranges-method Man page
as.list,EpiTxDb-method Man page
build_SQL_CREATE_modification2reaction_table Source code
build_SQL_CREATE_modification2reference_table Source code
build_SQL_CREATE_modification2specifier_table Source code
build_SQL_CREATE_modification_table Source code
build_SQL_CREATE_reaction_table Source code
build_SQL_CREATE_reference_table Source code
build_SQL_CREATE_seqnames_table Source code
build_SQL_CREATE_specifier_table Source code
columns Man page
columns,EpiTxDb-method Man page
compareEpiTxDbs Source code
downloadRMBaseFiles Man page Source code
getRMBaseDataAsGRanges Man page Source code
gettRNAdbDataAsGRanges Man page Source code
insert_data_into_table Source code
keys Man page
keys,EpiTxDb-method Man page
keytypes Man page
keytypes,EpiTxDb-method Man page
listAvailableGenomesFromRMBase Man page Source code
listAvailableModFromRMBase Man page Source code
listAvailableOrganismsFromRMBase Man page Source code
listAvailableOrganismsFromtRNAdb Man page Source code
load_modifications Source code
load_reactions Source code
load_references Source code
load_seqnames Source code
load_specifiers Source code
makeEpiTxDb Man page Source code
makeEpiTxDbFromGRanges Man page Source code
makeEpiTxDbFromRMBase Man page Source code
makeEpiTxDbFromRMBaseFiles Man page Source code
makeEpiTxDbFromtRNAdb Man page Source code
makeFeatureIds Source code
modifications Man page
modifications,EpiTxDb-method Man page
modificationsBy Man page
modificationsBy,EpiTxDb-method Man page
modifiedSeqsByTranscript Man page
modifiedSeqsByTranscript,EpiTxDb,DNAStringSet-method Man page
organism,EpiTxDb-method Man page
positionSequence Man page
positionSequence,Ranges-method Man page
positionSequence,RangesList-method Man page
rescale Man page
rescale,GRanges-method Man page
rescale,GRangesList-method Man page
rescale,IRanges-method Man page
rescale,IRangesList-method Man page
rmbase_data Man page
select Man page
select,EpiTxDb-method Man page
seqinfo,EpiTxDb-method Man page
seqlevels,EpiTxDb-method Man page
shiftGenomicToTranscript Man page
shiftGenomicToTranscript,GRanges,GRangesList-method Man page
shiftGenomicToTranscript,GRangesList,GRangesList-method Man page
shiftTranscriptToGenomic Man page
shiftTranscriptToGenomic,GRanges,GRangesList-method Man page
shiftTranscriptToGenomic,GRangesList,GRangesList-method Man page
translateCols Source code
FelixErnst/EpiTxDb documentation built on March 31, 2024, 1:21 a.m.

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