buildCDS                Reference-guided construction of CDS on GTF
                        object
chrom_matched_query_gtf
                        Chromosome matched version of "query_gtf"
domains.known           Example output of predictDomains()
domains.out             Example output of predictDomains()
filtereach              Internally filter each element of a
                        GenomicRangesList
has_consistentSeqlevels
                        Test consistency of chromosome naming styles
                        (aka seqlevels; e.g. "chr1" vs "1") across
                        multiple objects
importFASTA             Import FASTA file into R
importGTF               Import GTF file into R
matchChromosomes        Match seqlevels of input GRanges to reference
                        GRanges or BioString objects
matchGeneInfo           Match gene metadata from query GTF to a
                        reference GTF
matched_query_gtf       Seqlevels and gene_id matched query data
mutateeach              Internally create or transform metadata of a
                        GenomicRangesList
new_query_gtf           Query data containing CDS information
predictDomains          Predict protein domain families from coding
                        transcripts
predictNMD              Predict NMD sensitivity on mRNA transcripts
query_cds               CDS from 4 transcripts entries of the same gene
query_exons             GRangeList of exons from 4 transcripts entries
                        from query_gtf
query_gtf               Imported GTF file containing 4 transcript
                        entries of the same gene
ref_cds                 CDS from 2 reference transcripts entries of the
                        same gene
ref_exons               Exons from 2 reference transcripts entries of
                        the same gene
ref_gtf                 Imported GTF file containing 2 reference
                        transcript entries of the same gene
sorteach                Internally sort each element of a
                        GenomicRangesList
subsetNewTranscripts    Shortlist GTF GRanges object for new
                        transcripts
trimTranscripts         Resize 5' and 3' ends of a transcript
                        GenomicRanges
viewTranscripts         Plot transcripts directly from GTF.
