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

## Documentation for package ‘FLAMES’ version 1.3.4

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

## Help Pages

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_annotate_umap | FLAMES Annotated Plottings
sc_DTU_analysis | FLAMES Differential Transcript Usage Analysis
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