Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database. - Luke Zappia; Belinda Phipson; Alicia Oshlack (PLoS Comput. Biol., 2018)

Tools and techniques for single-cell RNA sequencing data. - Luke Zappia (2019)

HiTIME: An efficient model-selection approach for the detection of unknown drug metabolites in LC-MS data. - Michael G. Leeming; Andrew Paul Isaac; Luke Zappia; Richard A. J. O'hair; William A. Donald; Bernard J. Pope (SoftwareX, 2020)

1000 tools paper. - Luke Zappia; Fabian J. Theis (Zenodo, 2021)

1000 tools paper. - Luke Zappia; Fabian J. Theis (Zenodo, 2021)

Code for "Feature selection methods affect the performance of scRNA-seq data integration and querying". - Luke Zappia; Sabrina Richter; Ciro Ramírez-Suástegui; Raphael Kfuri-Rubens; Weixu Wang; Oliver Dietrich; Amit Frishberg; Malte D. Lücken; Fabian J. Theis (Zenodo, 2024)

funkyheatmap: Visualising data frames with mixed data types. - Robrecht Cannoodt; Louise Deconinck; Artuur Couckuyt; Nikolay S. Markov; Luke Zappia; Malte D. Lücken; Marta Interlandi; Yvan Saeys; Wouter Saelens (J. Open Source Softw., 2025)