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

## Documentation for package ‘FLAMES’ version 2.5.2

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

## 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.
BulkPipeline | Pipeline for bulk long read RNA-seq data processing
bulk_long_pipeline | Pipeline for bulk long read RNA-seq data processing (deprecated)
combine_sce | Combine SCE
config | Get pipeline configurations
config-method | Get pipeline configurations
config<- | Set pipeline configurations
config<--method | Set pipeline configurations
controllers | Get controllers
controllers-method | Get controllers
controllers<- | Set controllers
controllers<--method | Set controllers
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
example_pipeline | Example pipelins
experiment | Get pipeline results
experiment-method | Get pipeline results
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_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
index_genome | Index the reference genome for minimap2
index_genome-method | Index the reference genome for minimap2
load_config | Load Configurations
MultiSampleSCPipeline | Pipeline for multi-sample long-read scRNA-seq data
mutation_positions | Calculate mutation positions within the gene body
plot_coverage | plot read coverages
plot_demultiplex | Plot Cell Barcode demultiplex statistics
plot_demultiplex-method | Plot Cell Barcode demultiplex statistics
plot_durations | Plot pipeline step durations
plot_durations-method | Plot pipeline step durations
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
resume_FLAMES | Resume a FLAMES pipeline
resume_FLAMES-method | Resume a FLAMES pipeline
run_FLAMES | Execute a FLAMES pipeline
run_FLAMES-method | Execute a FLAMES pipeline
run_step | Execute a single step of the FLAMES pipeline
run_step-method | Execute a single step of the FLAMES pipeline
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_gene_entropy | Compute Gene Isoform Entropy Matrix
sc_genotype | Genotype a single-cell mutation
sc_impute_transcript | Impute missing transcript counts
sc_long_multisample_pipeline | Pipeline for Multi-sample Single Cell Data (deprecated)
sc_long_pipeline | Pipeline for Single Cell Data (deprecated)
sc_mutations | Variant count for single-cell data
sc_plot_genotype | Plot genotype of single-cell data
SingleCellPipeline | Pipeline for Single Cell Data
steps | Steps to perform in the pipeline
steps-method | Steps to perform in the pipeline
steps<- | Set steps to perform in the pipeline
steps<--method | Set steps to perform in the pipeline
weight_transcripts | Weight transcripts by read counts