buildCDS	buildCDS
chrom_matched_query_gtf	chrom_matched_query_gtf
domains.known	domains.known
domains.out	domains.out
filtereach	filtereach
has_consistentSeqlevels	has_consistentSeqlevels
importFASTA	importFASTA
importGTF	importGTF
matchChromosomes	matchChromosomes
matched_query_gtf	matched_query_gtf
matchGeneInfo	matchGeneInfo
mutateeach	mutateeach
new_query_gtf	new_query_gtf
predictDomains	predictDomains
predictNMD	predictNMD
query_cds	query_cds
query_exons	query_exons
query_gtf	query_gtf
ref_cds	ref_cds
ref_exons	ref_exons
ref_gtf	ref_gtf
sorteach	sorteach
subsetNewTranscripts	subsetNewTranscripts
trimTranscripts	trimTranscripts
viewTranscripts	viewTranscripts
