exonicParts |
Extract non-overlapping exonic or intronic parts from a TxDb-like object |
exons |
Extract genomic features from a TxDb-like object |
exons-method |
Extract genomic features from a TxDb-like object |
exonsBy |
Extract and group genomic features of a given type from a TxDb-like object |
exonsBy-method |
Extract and group genomic features of a given type from a TxDb-like object |
exonsByOverlaps |
Extract genomic features from a TxDb-like object based on their genomic location |
exonsByOverlaps-method |
Extract genomic features from a TxDb-like object based on their genomic location |
extendExonsIntoIntrons |
Extend exons by a given number of bases into their adjacent introns |
extractTranscriptSeqs |
Extract transcript (or CDS) sequences from chromosome sequences |
extractTranscriptSeqs-method |
Extract transcript (or CDS) sequences from chromosome sequences |
extractUpstreamSeqs |
Extract sequences upstream of a set of genes or transcripts |
extractUpstreamSeqs-method |
Extract sequences upstream of a set of genes or transcripts |
makeFDbPackageFromUCSC |
[Moved to txdbmaker] Making a TxDb package from annotations available at the UCSC Genome Browser, biomaRt or from another source. |
makeFeatureDbFromUCSC |
[Moved to txdbmaker] Make a FeatureDb object from annotations available at the UCSC Genome Browser |
makePackageName |
[Moved to txdbmaker] Making a TxDb package from annotations available at the UCSC Genome Browser, biomaRt or from another source. |
makeTxDb |
[Moved to txdbmaker] Make a TxDb object from user supplied annotations |
makeTxDbFromBiomart |
[Moved to txdbmaker] Make a TxDb object from annotations available on a BioMart database |
makeTxDbFromEnsembl |
[Moved to txdbmaker] Make a TxDb object from an Ensembl database |
makeTxDbFromGFF |
[Moved to txdbmaker] Make a TxDb object from annotations available as a GFF3 or GTF file |
makeTxDbFromGRanges |
[Moved to txdbmaker] Make a TxDb object from a GRanges object |
makeTxDbFromUCSC |
[Moved to txdbmaker] Make a TxDb object from annotations available at the UCSC Genome Browser |
makeTxDbPackage |
[Moved to txdbmaker] Making a TxDb package from annotations available at the UCSC Genome Browser, biomaRt or from another source. |
makeTxDbPackageFromBiomart |
[Moved to txdbmaker] Making a TxDb package from annotations available at the UCSC Genome Browser, biomaRt or from another source. |
makeTxDbPackageFromUCSC |
[Moved to txdbmaker] Making a TxDb package from annotations available at the UCSC Genome Browser, biomaRt or from another source. |
mapFromTranscripts |
Map range coordinates between transcripts and genome space |
mapFromTranscripts-method |
Map range coordinates between transcripts and genome space |
mapIdsToRanges |
Map IDs to Genomic Ranges |
mapIdsToRanges-method |
Map IDs to Genomic Ranges |
mapRangesToIds |
Map Genomic Ranges to IDs |
mapRangesToIds-method |
Map Genomic Ranges to IDs |
mapToTranscripts |
Map range coordinates between transcripts and genome space |
mapToTranscripts-method |
Map range coordinates between transcripts and genome space |
microRNAs |
Extract microRNA or tRNA genomic ranges from an object |
microRNAs-method |
Extract microRNA or tRNA genomic ranges from an object |
terminators |
Extract genomic features from a TxDb-like object |
terminators-method |
Extract genomic features from a TxDb-like object |
threeUTRsByTranscript |
Extract and group genomic features of a given type from a TxDb-like object |
threeUTRsByTranscript-method |
Extract and group genomic features of a given type from a TxDb-like object |
tidyExons |
Extract non-overlapping exonic or intronic parts from a TxDb-like object |
tidyIntrons |
Extract non-overlapping exonic or intronic parts from a TxDb-like object |
tidyTranscripts |
Extract non-overlapping exonic or intronic parts from a TxDb-like object |
transcriptLengths |
Extract the transcript lengths (and other metrics) from a TxDb object |
transcriptLocs2refLocs |
Converting transcript-based locations into reference-based locations |
transcripts |
Extract genomic features from a TxDb-like object |
transcripts-method |
Extract genomic features from a TxDb-like object |
transcriptsBy |
Extract and group genomic features of a given type from a TxDb-like object |
transcriptsBy-method |
Extract and group genomic features of a given type from a TxDb-like object |
transcriptsByOverlaps |
Extract genomic features from a TxDb-like object based on their genomic location |
transcriptsByOverlaps-method |
Extract genomic features from a TxDb-like object based on their genomic location |
transcriptWidths |
Converting transcript-based locations into reference-based locations |
tRNAs |
Extract microRNA or tRNA genomic ranges from an object |
tRNAs-method |
Extract microRNA or tRNA genomic ranges from an object |
TxDb |
TxDb objects |
TxDb-class |
TxDb objects |