add_gene_counts         Add gene counts to a 'SingleCellExperiment'
                        object
annotation_to_fasta     GTF/GFF to FASTA conversion
barcode_group           Create a Flexiplex barcode group
barcode_segment         Create a Flexiplex barcode segment
blaze                   BLAZE Assign reads to cell barcodes.
bulk_long_pipeline      Pipeline for bulk long read RNA-seq data
                        processing (deprecated)
BulkPipeline            Pipeline for bulk long read RNA-seq data
                        processing
combine_sce             Combine SCE
config                  Get pipeline configurations
config<-                Set pipeline configurations
controllers             Get controllers
controllers<-           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
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_diversity          Compute Gene Isoform Entropy Matrix
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
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_durations          Plot pipeline step durations
plot_isoform_heatmap    FLAMES heetmap plots
plot_isoform_reduced_dim
                        FLAMES isoform reduced dimensions plots
plot_isoforms           Plot isoforms
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
run_FLAMES              Execute a FLAMES pipeline
run_step                Execute a single step of the FLAMES pipeline
sc_DTU_analysis         FLAMES Differential Transcript Usage Analysis
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
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
SingleCellPipeline      Pipeline for Single Cell Data
steps                   Steps to perform in the pipeline
steps<-                 Set steps to perform in the pipeline
weight_transcripts      Weight transcripts by read counts
