.get_velocity_files     Generate RNA velocity files for GRanges
EC2gene                 Map EC Index to Genes Compatible with the EC
annot_circular          Transfer information about circular chromosomes
                        between genome and annotation
annots_from_fa_df       Get genome annotation from Ensembl FASTA file
cellranger_biotypes     Cell Ranger gene biotypes
check_char1             Check that an object is a character vector of
                        length 1
check_genome            Check for chromosomes in genome but not
                        annotation
check_gff               Check inputs to tr2g_gtf and tr2g_gff3
check_tag_present       Check that a tag is present in attribute field
                        of GTF/GFF
check_tx                Check if transcript ID in transcriptome and
                        annotation match
dl_transcriptome        Download transcriptome from Ensembl
ensembl_gene_biotypes   Gene biotypes from Ensembl
ensembl_gff_mcols       These are the column names of the 'mcols' when
                        the Ensembl GTF file is read into R as a
                        'GRanges', including 'gene_id',
                        'transcript_id', 'biotype', 'description', and
                        so on, and the mandatory tags like 'ID',
                        'Name', and 'Parent'.
ensembl_gtf_mcols       Tags in the attributes field of Ensembl GTF
                        files
ensembl_tx_biotypes     Transcript biotypes from Ensembl
get_intron_flanks       Get flanked intronic ranges
get_knee_df             Plot the transposed knee plot and inflection
                        point
get_velocity_files      Get files required for RNA velocity with
                        bustools
make_sparse_matrix      Convert the Output of 'kallisto bus' into Gene
                        by Gell Matrix
match_style             Match chromosome naming styles of annotation
                        and genome
read_count_output       Read matrix along with barcode and gene names
read_velocity_output    Read intronic and exonic matrices into R
refseq_gff_mcols        Tags in the attributes field of RefSeq GFF
                        files
save_tr2g_bustools      Save transcript to gene file for use in
                        'bustools'
sort_tr2g               Sort transcripts to the same order as in
                        kallisto index
species2dataset         Convert Latin species name to dataset name
standardize_tags        Standardize GRanges field names
sub_annot               Remove chromosomes in anotation absent from
                        genome
subset_annot            Subset genome annotation
tr2g_EnsDb              Get transcript and gene info from EnsDb objects
tr2g_GRanges            Get transcript and gene info from GRanges
tr2g_TxDb               Get transcript and gene info from TxDb objects
tr2g_ensembl            Get transcript and gene info from Ensembl
tr2g_fasta              Get transcript and gene info from names in
                        FASTA files
tr2g_gff3               Get transcript and gene info from GFF3 file
tr2g_gtf                Get transcript and gene info from GTF file
tr2g_junction           tr2g for exon-exon junctions
transcript2gene         Map Ensembl transcript ID to gene ID
validate_velocity_input
                        Validate input to get_velocity_files
write_velocity_output   Write the files for RNA velocity to disk
