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

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Documentation for package ‘FLAMES’ version 1.11.0

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

Help Pages

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
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
cutadapt	cutadapt wrapper
demultiplex_sockeye	Demultiplex reads using Sockeye outputs
filter_annotation	filter annotation for plotting coverages
find_barcode	Match Cell Barcodes
find_isoform	Isoform identification
find_variants	bulk variant identification
FLAMES	FLAMES: full-length analysis of mutations and splicing
flexiplex	Rcpp port of flexiplex
get_GRangesList	Parse FLAMES' GFF output
minimap2_align	Minimap2 Align to Genome
minimap2_realign	Minimap2 re-align reads to transcriptome
parse_gff_tree	Parse Gff3 file
plot_coverage	plot read coverages
plot_demultiplex	Plot Cell Barcode demultiplex statistics
quantify_gene	Gene quantification
quantify_transcript	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_heatmap_expression	FLAMES heetmap plots
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
sc_reduce_dims	runPCA and runUMAP wrapper
sc_umap_expression	FLAMES UMAP plots
sys_which	Sys.which wrapper Wrapper for Sys.which that replaces "" with NA