| bulk_long_pipeline | Pipeline for Bulk Data |
| bulk_windows_pipeline_setup | FLAMES Windows Bulk Pipeline |
| callBasilisk | Internal utility function for simplifying calls to basiliskRun using a given basilisk environment |
| create_config | Create Configuration File From Arguments |
| generate_umap | Generate UMAP plot |
| generic_long_pipeline | Generic FLAMES pipeline |
| get_default_config_file | Default Configuration File |
| gff3_to_bed12 | GFF3 to BED12 |
| match_cell_barcode | Match Cell Barcodes |
| merge_bulk_fastq | Merge FASTQ |
| merge_bulk_fastq_cpp | Merge Bulk Fastq Files |
| merge_bulk_fastq_python | Merge FASTQ using python. Depreciated |
| minimap2_align | Minimap2 Align to Genome |
| minimap2_check_callable | Check if minimap2 is available |
| parse_gff_tree | Parse Gff3 file |
| parse_json_config | Parse Json Configuration File |
| print_config | Print Configuration File |
| samtools_as_bam | Samtools as BAM |
| samtools_sort_index | Samtools Sort and Index |
| sc_DTU_analysis | FLAMES Differential Transcript Usage Analysis |
| sc_long_pipeline | Pipeline for Single Cell Data |
| sc_mutations | FLAMES variant calling |
| sc_windows_pipeline_setup | Windows Single Cell FLAMES Pipeline |
| windows_pipeline_isoforms | Windows Pipeline - Find Isoforms |
| windows_pipeline_quantification | Windows Pipeline - Quantification |
| write_config | Write Configuration Dictionary to File |