FLAMES (FLAMESv2)

FLAMES v2.6.0 (Bioconductor 3.23) is a modular, protocol-agnostic R/Bioconductor package for full-length isoform analysis from long-read single-cell and spatial RNA-seq data. It supports droplet-based and combinatorial barcoding single-cell methods as well as spatial transcriptomics workflows, and scales to multi-sample cohort analyses. Key outputs include isoform detection, alternative splicing quantification, and differential splicing analysis integrated with Bioconductor's genomic infrastructure.

FLAMES v2 — Long-Read Single-Cell & Spatial RNA-seq Isoform Analysis

Version 2.6.0 in Bioconductor 3.23 (R ≥ 4.6). Full Length Analysis of Mutations and Splicing for bulk and single-cell long-read RNA-seq.

Supports Nanopore and PacBio long-read data
Compatible with droplet-based (10x), combinatorial barcoding, and spatial transcriptomics protocols
Automated pipelines + intermediate functions for custom workflows
Alternative splicing detection and differential splicing analysis
Multi-sample / multi-condition cohort scaling
License: GPL ≥ 3 | Maintainer: Changqing Wang (Ritchie Lab)