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 |