Mei R. M. Du

FLAMESv2 is a flexible R/Bioconductor package for analyzing long-read single-cell RNA-seq data, demonstrating field-leading performance in isoform analysis and cell-type identification.

Benchmarking six long-read RNA-seq protocol-platform combinations and 14 tools across human, mouse, and manatee shows read length and accuracy drive isoform detection, depth drives quantification.

The paper benchmarks spatial transcriptomics technologies using a multi-sample dataset from mouse spleen tissue, finding improved data quality with probe-based capture methods and CytAssist.

scPipe provides a preprocessing pipeline for single-cell ATAC-Seq and multi-modal data in R/Bioconductor, enabling quality control and downstream analysis.

The paper benchmarks long-read RNA-sequencing tools using synthetic data to evaluate isoform detection and differential expression analysis performance.

The paper develops FLT-seq and FLAMES to characterize full-length isoforms in single cells of human and mouse, identifying thousands of unannotated isoforms and linking them to functional modules and drug resistance mutations.