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

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Documentation for package ‘FLAMES’ version 2.3.3

• 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.
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
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
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_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_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
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