GenomicFeatures

FeatureDb objects

TxDb objects

Coerce to file format structures

Map range coordinates between transcripts and genome space

Compute coverage by transcript (or CDS) of a set of ranges

Extract non-overlapping exon parts from an object

Extract non-overlapping exonic or intronic parts from a TxDb-like object

Extract transcript (or CDS) sequences from chromosome sequences

Extract sequences upstream of a set of genes or transcripts

Extract simple features from a FeatureDb object

Get gene promoter sequences

Map internal ids to external names for a given feature type

Making a FeatureDb object from annotations available at the UCSC Genome Browser

Making a TxDb object from user supplied annotations

Make a TxDb object from annotations available on a BioMart database

Make a TxDb object from an Ensembl database

Make a TxDb object from annotations available as a GFF3 or GTF file

Make a TxDb object from a GRanges object

Make a TxDb object from annotations available at the UCSC Genome Browser

Making a TxDb package from annotations available at the UCSC Genome Browser, biomaRt or from another source.

Map IDs to Genomic Ranges

Map Genomic Ranges to IDs

Extract microRNA or tRNA genomic ranges from an object

Finding the nearest genomic range neighbor in a TxDb

Using the "select" interface on TxDb objects

Extract the transcript lengths (and other metrics) from a TxDb object

Converting transcript-based locations into reference-based locations

Extract genomic features from a TxDb-like object

Extract and group genomic features of a given type from a TxDb-like object

Extract genomic features from a TxDb-like object based on their genomic location