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

## Documentation for package ‘FLAMES’ version 1.10.3

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

## Help Pages

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
find_variants | bulk variant identification
FLAMES | FLAMES: full-length analysis of mutations and splicing
flexiplex | Rcpp port of flexiplex
get_GRangesList | Parse FLAMES' GFF output
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 | Variant count for single-cell data
sc_reduce_dims | runPCA and runUMAP wrapper
sc_umap_expression | FLAMES UMAP plots
sys_which | Sys.which wrapper Wrapper for Sys.which that replaces "" with NA