The FLAMES package provides a framework for performing single-cell and bulk read full-length analysis of mutations and splicing. FLAMES performs cell barcode and UMI assignment from nanopore reads as well as semi-supervised isoform detection and quantification. FLAMES is designed to be an easy and quick to use, powerful workflow for isoform detection and quantification, splicing analysis and mutation detection, and seeks to overcome the limitations of other tools, such as an inability to process single cell data, and a focus on cell barcode and UMI assignment (Tian et al. 2020).

This R package represents an enhanced iteration of the FLAMES Python module that originally designed to support the research work presented in Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing by Tian et al (2020). This upgraded R version not only simplifies the installation and execution processes but also incorporates additional functionality, streamlining the analysis of single-cell full-length isoforms using long-read sequencing data.