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| .get_velocity_files | Generate RNA velocity files for GRanges |
| annots_from_fa_df | Get genome annotation from Ensembl FASTA file |
| annots_from_fa_GRanges | Get genome annotation from Ensembl FASTA file |
| annot_circular | Transfer information about circular chromosomes between genome and annotation |
| 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 |
| EC2gene | Map EC Index to Genes Compatible with the EC |
| 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_inflection | Plot the transposed knee plot and inflection point |
| 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 |
| get_velocity_files-method | Get files required for RNA velocity with bustools |
| knee_plot | Plot the transposed knee plot and inflection point |
| 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 |
| subset_annot | Subset genome annotation |
| subset_annot-method | Subset genome annotation |
| sub_annot | Remove chromosomes in anotation absent from genome |
| tr2g_EnsDb | Get transcript and gene info from EnsDb 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_GRanges | Get transcript and gene info from GRanges |
| tr2g_gtf | Get transcript and gene info from GTF file |
| tr2g_junction | tr2g for exon-exon junctions |
| tr2g_TxDb | Get transcript and gene info from TxDb objects |
| 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 |