.legacy_pattern_to_flexiplex_segments	dot-legacy_pattern_to_flexiplex_segments
.resolve_bc_lists	dot-resolve_bc_lists
addRowRanges	addRowRanges
add_gene_counts	add_gene_counts
annotation_to_fasta	annotation_to_fasta
barcode_group	barcode_group
barcode_segment	barcode_segment
blaze	blaze
BulkPipeline	BulkPipeline
bulk_long_pipeline	bulk_long_pipeline
combine_sce	combine_sce
config	config
config,FLAMES.Pipeline-method	config
config<-	config-set
config<-,FLAMES.Pipeline-method	config-set
controllers	controllers
controllers,FLAMES.Pipeline-method	controllers
controllers<-	controllers-set
controllers<-,FLAMES.Pipeline-method	controllers-set
convolution_filter	convolution_filter
create_config	create_config
create_sce_from_dir	create_sce_from_dir
create_se_from_dir	create_se_from_dir
create_spe	create_spe
cutadapt	cutadapt
demultiplex_sockeye	demultiplex_sockeye
example_pipeline	example_pipeline
experiment	experiment
experiment,FLAMES.Pipeline-method	experiment
fake_stranded_gff	fake_stranded_gff
filter_annotation	filter_annotation
filter_coverage	filter_coverage
find_barcode	find_barcode
find_bin	find_bin
find_diversity	find_diversity
find_isoform	find_isoform
find_variants	find_variants
FLAMES	FLAMES
flexiplex	flexiplex
get_coverage	get_coverage
get_GRangesList	get_GRangesList
gff2bed	gff2bed
index_genome	index_genome
index_genome,FLAMES.Pipeline-method	index_genome
load_config	load_config
merge_configs_recursive	merge_configs_recursive
minimap2_align	minimap2_align
MultiSampleSCPipeline	MultiSampleSCPipeline
mutation_positions	mutation_positions
mutation_positions_single	mutation_positions_single
plot_coverage	plot_coverage
plot_demultiplex	plot_demultiplex
plot_demultiplex,FLAMES.SingleCellPipeline-method	plot_demultiplex
plot_demultiplex_raw	plot_demultiplex_raw
plot_durations	plot_durations
plot_durations,FLAMES.Pipeline-method	plot_durations
plot_isoforms	plot_isoforms
plot_isoform_heatmap	plot_isoform_heatmap
plot_isoform_reduced_dim	plot_isoform_reduced_dim
plot_spatial_feature	plot_spatial_feature
plot_spatial_isoform	plot_spatial_isoform
plot_spatial_pie	plot_spatial_pie
quantify_gene	quantify_gene
quantify_transcript	quantify_transcript
quantify_transcript_flames	quantify_transcript_flames
resume_FLAMES	resume_FLAMES
resume_FLAMES,FLAMES.Pipeline-method	resume_FLAMES
run_FLAMES	run_FLAMES
run_FLAMES,FLAMES.Pipeline-method	run_FLAMES
run_step	run_step
run_step,FLAMES.Pipeline-method	run_step
scmixology_lib10	scmixology_lib10
scmixology_lib10_transcripts	scmixology_lib10_transcripts
scmixology_lib90	scmixology_lib90
sc_DTU_analysis	sc_DTU_analysis
sc_genotype	sc_genotype
sc_impute_transcript	sc_impute_transcript
sc_long_multisample_pipeline	sc_long_multisample_pipeline
sc_long_pipeline	sc_long_pipeline
sc_mutations	sc_mutations
sc_plot_genotype	sc_plot_genotype
set_nested_param	set_nested_param
show,FLAMES.MultiSampleSCPipeline-method	show-FLAMESPipeline
show,FLAMES.Pipeline-method	show-FLAMESPipeline
show,FLAMES.SingleCellPipeline-method	show-FLAMESPipeline
SingleCellPipeline	SingleCellPipeline
steps	steps
steps,FLAMES.Pipeline-method	steps
steps<-	steps-set
steps<-,FLAMES.Pipeline-method	steps-set
weight_transcripts	weight_transcripts
