Jiayi Wang

The paper benchmarks small variant calling pipelines for long-read RNA sequencing data, finding that sequencing quality is the main factor affecting performance, followed by variant caller and alignment strategy.

The paper introduces three R/bioconductor packages to address technical variations in ATAC-seq data and improve motif accessibility analysis.

rhapsodist processes BD Rhapsody scRNA-seq data using a Snakemake workflow, enabling cross-aligner comparison and generating count tables in SingleCellExperiment format.

The paper improves single-cell differential expression analysis by integrating bulk RNA-seq data through bulk-based hypothesis weighing, enhancing power and robustness.

The paper develops a hybrid sequencing strategy combining short-read and long-read methods to enhance genotype-phenotype analysis at single-cell resolution.

The paper benchmarks methods for identifying differentially-active transcription factors from ATAC-seq data using curated and simulated datasets, identifying three promising approaches.