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
create_sce_from_dir     Create 'SingleCellExperiment' object from
                        'FLAMES' output folder
create_se_from_dir      Create 'SummarizedExperiment' object from
                        'FLAMES' output folder
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_cpp
                        Match Cell Barcodes
merge_bulk_fastq        Merge FASTQ
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_annotate_umap        FLAMES Annotated Plottings
sc_long_multisample_pipeline
                        Pipeline for Multi-sample Single Cell Data
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
