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 | 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_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_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 |
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