| annotation_to_fasta | GTF/GFF to FASTA conversion |
| blaze | BLAZE Assign reads to cell barcodes. |
| bulk_long_pipeline | Pipeline for Bulk Data |
| combine_sce | Combine SCE |
| 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 |
| cutadapt | cutadapt wrapper |
| demultiplex_sockeye | Demultiplex reads using Sockeye outputs |
| filter_annotation | filter annotation for plotting coverages |
| find_barcode | Match Cell Barcodes |
| find_isoform | Isoform identification |
| FLAMES | FLAMES: full-length analysis of mutations and splicing |
| flexiplex | Rcpp port of flexiplex |
| get_GRangesList | Parse FLAMES' GFF output |
| locate_minimap2_dir | locate parent folder of minimap2 |
| minimap2_align | Minimap2 Align to Genome |
| minimap2_realign | Minimap2 re-align reads to transcriptome |
| parse_gff_tree | Parse Gff3 file |
| plot_coverage | plot read coverages |
| plot_demultiplex | Plot Cell Barcode demultiplex statistics |
| quantify_gene | Gene quantification |
| quantify_transcript | Transcript quantification |
| scmixology_lib10 | scMixology short-read gene counts - sample 2 |
| scmixology_lib10_transcripts | scMixology long-read transcript counts - sample 2 |
| scmixology_lib90 | scMixology short-read gene counts - sample 1 |
| sc_DTU_analysis | FLAMES Differential Transcript Usage Analysis |
| sc_heatmap_expression | FLAMES heetmap plots |
| 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_reduce_dims | runPCA and runUMAP wrapper |
| sc_umap_expression | FLAMES UMAP plots |