Package index • FLAMES

About FLAMES

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

Pipelines

BulkPipeline(): Pipeline for bulk long read RNA-seq data processing
SingleCellPipeline(): Pipeline for Single Cell Data
MultiSampleSCPipeline(): Pipeline for multi-sample long-read scRNA-seq data
example_pipeline(): Example pipelins

Pipeline execution

run_FLAMES(): Execute a FLAMES pipeline
resume_FLAMES(): Resume a FLAMES pipeline
run_step(): Execute a single step of the FLAMES pipeline

Inspecting pipelines

steps(): Steps to perform in the pipeline
`steps<-`(): Set steps to perform in the pipeline
config(): Get pipeline configurations
`config<-`(): Set pipeline configurations
controllers(): Get controllers
`controllers<-`(): Set controllers
experiment(): Get pipeline results
plot_durations(): Plot pipeline step durations

Barcode demultiplexing

find_barcode(): Match Cell Barcodes
blaze(): BLAZE Assign reads to cell barcodes.
flexiplex(): Rcpp port of flexiplex
cutadapt(): cutadapt wrapper

Alignment

annotation_to_fasta(): GTF/GFF to FASTA conversion
index_genome(): Index the reference genome for minimap2

Transcript identification

find_isoform(): Isoform identification

Quantification

quantify_gene(): Gene quantification
quantify_transcript(): Transcript quantification
quantify_transcript_flames(): FLAMES Transcript quantification

Mutation analysis

find_variants(): bulk variant identification
sc_mutations(): Variant count for single-cell data
sc_genotype(): Genotype a single-cell mutation
mutation_positions(): Calculate mutation positions within the gene body

Visualization

plot_coverage(): plot read coverages
plot_demultiplex(): Plot Cell Barcode demultiplex statistics
plot_isoform_heatmap(): FLAMES heetmap plots
plot_isoform_reduced_dim(): FLAMES isoform reduced dimensions plots
plot_isoforms(): Plot isoforms
sc_plot_genotype(): Plot genotype of single-cell data

Alignment coverages

get_coverage(): Get read coverages from BAM file
filter_coverage(): Filter transcript coverage
convolution_filter(): Convolution filter for smoothing transcript coverages
weight_transcripts(): Weight transcripts by read counts

Analysis of FLT-seq sub-samlped data

combine_sce(): Combine SCE
sc_impute_transcript(): Impute missing transcript counts

Analysis of spatial transcriptomics data

create_spe(): Create a SpatialExperiment object
plot_spatial_isoform(): Plot spatial pie chart of isoforms
plot_spatial_pie(): Plot spatial pie chart
plot_spatial_feature(): Plot feature on spatial image

Analysis of single-cell data

sc_gene_entropy(): Compute Gene Isoform Entropy Matrix
sc_DTU_analysis(): FLAMES Differential Transcript Usage Analysis

Miscellaneous

add_gene_counts(): Add gene counts to a SingleCellExperiment object
create_config(): Create Configuration File From Arguments
load_config(): Load Configurations
create_sce_from_dir(): Create SingleCellExperiment object from FLAMES output folder
create_se_from_dir(): Create SummarizedExperiment object from FLAMES output folder
filter_annotation(): filter annotation for plotting coverages
get_GRangesList(): Parse FLAMES' GFF output
demultiplex_sockeye(): Demultiplex reads using Sockeye outputs
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
find_bin(): Find path to a binary Wrapper for Sys.which to find path to a binary

Pipelines (deprecated)

sc_long_pipeline(): Pipeline for Single Cell Data (deprecated)
sc_long_multisample_pipeline(): Pipeline for Multi-sample Single Cell Data (deprecated)
bulk_long_pipeline(): Pipeline for bulk long read RNA-seq data processing (deprecated)