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

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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