# FLAMES: Full Length Analysis of Mutations and Splicing in long read RNA-seq data

## Documentation for package ‘FLAMES’ version 1.6.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

annotation_to_fasta | GTF/GFF to FASTA conversion
barcode_info_plots | Barcode demultiplexing QC plots
bulk_long_pipeline | Pipeline for Bulk Data
callBasilisk | Internal utility function for simplifying calls to basiliskRun using a given basilisk environment
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
demultiplex_sockeye | Demultiplex reads using Sockeye outputs
find_barcode | Match Cell Barcodes
find_isoform | Isoform identification
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
quantify | Transcript quantification
sc_annotate_plots | FLAMES Annotated Plottings
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_umap_expression | FLAMES UMAP plots