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

experiment(): Get pipeline results

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

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

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

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

Miscellaneous

add_gene_counts(): Add gene counts to a SingleCellExperiment object

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

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)