Man pages for jmacdon/GenomicFeatures
Conveniently import and query gene models
| as-format-methods | Coerce to file format structures |
| coordinate-mapping-methods | Map range coordinates between transcripts and genome space |
| 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... |
| extractUpstreamSeqs | Extract sequences upstream of a set of genes or transcripts |
| FeatureDb-class | FeatureDb objects |
| features | Extract simple features from a FeatureDb object |
| getPromoterSeq-methods | Get gene promoter sequences |
| id2name | Map internal ids to external names for a given feature type |
| makeFeatureDbFromUCSC | Making a FeatureDb object from annotations available at the... |
| makeTxDb | Making a TxDb object from user supplied annotations |
| makeTxDbFromBiomart | Make a TxDb object from annotations available on a BioMart... |
| makeTxDbFromEnsembl | Make a TxDb object from an Ensembl database |
| makeTxDbFromGFF | Make a TxDb object from annotations available as a GFF3 or... |
| makeTxDbFromGRanges | Make a TxDb object from a GRanges object |
| makeTxDbFromUCSC | Make a TxDb object from annotations available at the UCSC... |
| makeTxDbPackage | Making a TxDb package from annotations available at the UCSC... |
| mapIdsToRanges | Map IDs to Genomic Ranges |
| mapRangesToIds | Map Genomic Ranges to IDs |
| microRNAs | Extract microRNA or tRNA genomic ranges from an object |
| nearest-methods | Finding the nearest genomic range neighbor in a TxDb |
| select-methods | Using the "select" interface on TxDb objects |
| transcriptLengths | Extract the transcript lengths (and other metrics) from a... |
| transcriptLocs2refLocs | Converting transcript-based locations into reference-based... |
| transcripts | Extract genomic features from a TxDb-like object |
| transcriptsBy | Extract and group genomic features of a given type from a... |
| transcriptsByOverlaps | Extract genomic features from a TxDb-like object based on... |
| TxDb-class | TxDb objects |
