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

## Documentation for package ‘FLAMES’ version 2.2.0

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

## Help Pages

add_gene_counts | Add gene counts to a 'SingleCellExperiment' object
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
convolution_filter | Convolution filter for smoothing transcript coverages
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
create_spe | Create a SpatialExperiment object
cutadapt | cutadapt wrapper
demultiplex_sockeye | Demultiplex reads using Sockeye outputs
filter_annotation | filter annotation for plotting coverages
filter_coverage | Filter transcript coverage
find_barcode | Match Cell Barcodes
find_bin | Find path to a binary Wrapper for Sys.which to find path to a binary
find_isoform | Isoform identification
find_variants | bulk variant identification
FLAMES | FLAMES: full-length analysis of mutations and splicing
flexiplex | Rcpp port of flexiplex
get_coverage | Get read coverages from BAM file
get_GRangesList | Parse FLAMES' GFF output
minimap2_align | Minimap2 Align to Genome
minimap2_realign | Minimap2 re-align reads to transcriptome
mutation_positions | Calculate mutation positions within the gene body
plot_coverage | plot read coverages
plot_demultiplex | Plot Cell Barcode demultiplex statistics
plot_isoforms | Plot isoforms
plot_isoform_heatmap | FLAMES heetmap plots
plot_isoform_reduced_dim | FLAMES isoform reduced dimensions plots
plot_spatial_feature | Plot feature on spatial image
plot_spatial_isoform | Plot spatial pie chart of isoforms
quantify_gene | Gene quantification
quantify_transcript | Transcript quantification
quantify_transcript_flames | FLAMES 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_impute_transcript | Impute missing transcript counts
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
weight_transcripts | Weight transcripts by read counts