Ron Stewart

CHARTS: A web application for characterizing and comparing tumor subpopulations in publicly available single-cell RNA-seq datasets

CHARTS provides a web tool to analyze and compare tumor subpopulations across public scRNA-seq cancer datasets.

scDD: A statistical approach for identifying differential distributions in single-cell RNA-seq experiments

scDD identifies differential expression patterns in single-cell RNA-seq by modeling complex distribution differences, outperforming existing methods in detecting subtle gene expression changes.

SCPattern: A statistical approach to identify and classify expression changes in single cell RNA-seq experiments with ordered conditions

SCPattern identifies and classifies expression changes in ordered scRNA-seq experiments using an empirical Bayes model with non-parametric statistics.

OEFinder: A user interface to identify and visualize ordering effects in single-cell RNA-seq data

OEFinder identifies and visualizes ordering effects in Fluidigm C1 single-cell RNA-seq data to detect potential artifacts.

Evaluation of de novo transcriptome assemblies from RNA-Seq data

The paper introduces RSEM-EVAL, a model-based score to evaluate de novo RNA-Seq assemblies, and demonstrates its effectiveness using axolotl limb regeneration data.