Bioconductor/GenomicFeatures
Tools for making and manipulating transcript centric annotations

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Man pages
31
Popular Man pages
coverageByTranscript: Compute coverage by transcript (or CDS) of a set of ranges disjointExons: Extract non-overlapping exon parts from an object exonicParts: Extract non-overlapping exonic or intronic parts from a... extractTranscriptSeqs: Extract transcript (or CDS) sequences from chromosome... FeatureDb-class: FeatureDb objects makeTxDbFromEnsembl: Make a TxDb object from an Ensembl database mapRangesToIds: Map Genomic Ranges to IDs
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API
461
Popular API
cdsByOverlaps,TxDb-method cdsByOverlaps exonsByOverlaps,TxDb-method exonsByOverlaps transcriptsByOverlaps,TxDb-method transcriptsByOverlaps threeUTRsByTranscript,TxDb-method
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Source code
54
Popular Source code
tests/run_unitTests.R inst/unitTests/test_transcriptsByOverlaps.R inst/unitTests/test_transcriptsBy.R inst/unitTests/test_transcripts.R inst/unitTests/test_select-methods.R inst/unitTests/test_mapIdsToRanges.R inst/unitTests/test_makeTxDbFromUCSC.R
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Bioconductor/GenomicFeatures: Tools for making and manipulating transcript centric annotations
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API

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 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
Bioconductor/GenomicFeatures documentation built on April 19, 2018, 5:25 p.m.

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