Package index • FLAMES

About FLAMES

FLAMES: FLAMES: full-length analysis of mutations and splicing

Pipelines

sc_long_pipeline(): Pipeline for Single Cell Data

sc_long_multisample_pipeline(): Pipeline for Multi-sample Single Cell Data

bulk_long_pipeline(): Pipeline for Bulk Data

Barcode demultiplexing

find_barcode(): Match Cell Barcodes

blaze(): BLAZE Assign reads to cell barcodes.

flexiplex(): Rcpp port of flexiplex

cutadapt(): cutadapt wrapper

Alignment

minimap2_align(): Minimap2 Align to Genome

minimap2_realign(): Minimap2 re-align reads to transcriptome

annotation_to_fasta(): GTF/GFF to FASTA conversion

Transcript identification

find_isoform(): Isoform identification

Quantification

quantify_gene(): Gene quantification

quantify_transcript(): Transcript quantification

Mutation calling

find_variants(): bulk variant identification

sc_mutations(): Variant count for single-cell data

Visualization

plot_coverage(): plot read coverages

plot_isoform_heatmap(): FLAMES heetmap plots

plot_isoform_reduced_dim(): FLAMES isoform reduced dimensions plots

plot_isoforms(): Plot isoforms

Analysis of FLT-seq sub-samlped data

combine_sce(): Combine SCE

sc_impute_transcript(): Impute missing transcript counts

Miscellaneous

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

sc_DTU_analysis(): FLAMES Differential Transcript Usage Analysis

filter_annotation(): filter annotation for plotting coverages

get_GRangesList(): Parse FLAMES' GFF output

demultiplex_sockeye(): Demultiplex reads using Sockeye outputs

parse_gff_tree(): Parse Gff3 file

plot_demultiplex(): Plot Cell Barcode demultiplex statistics

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

sys_which(): Sys.which wrapper Wrapper for Sys.which that replaces "" with NA