Socrates: identification of genomic rearrangements in tumour genomes by re-aligning soft clipped reads. - Jan Schröder; Arthur L. Hsu; Samantha E. Boyle; Geoff MacIntyre; Marek Cmero; Richard W. Tothill; Ricky W. Johnstone; Mark Shackleton; Anthony T. Papenfuss (Bioinform., 2014)

HYSYS: have you swapped your samples? - Jan Schröder; Vincent Corbin; Anthony T. Papenfuss (Bioinform., 2017)

Canary: an atomic pipeline for clinical amplicon assays. - Kenneth D. Doig; Jason Ellul; Andrew Fellowes; Ella R. Thompson; Georgina L. Ryland; Piers Blombery; Anthony T. Papenfuss; Stephen B. Fox (BMC Bioinform., 2017)

CLOVE: classification of genomic fusions into structural variation events. - Jan Schröder; Adrianto Wirawan; Bertil Schmidt; Anthony T. Papenfuss (BMC Bioinform., 2017)

tidyHeatmap: an R package for modular heatmap production based on tidy principles. - Stefano Mangiola; Anthony T. Papenfuss (J. Open Source Softw., 2020)

VIRUSBreakend: Viral Integration Recognition Using Single Breakends. - Daniel Cameron; Nina Jacobs; Paul Roepman; Peter Priestley; Edwin Cuppen; Anthony T. Papenfuss (Bioinform., 2021)

Interfacing Seurat with the R tidy universe. - Stefano Mangiola; Maria A. Doyle; Anthony T. Papenfuss (Bioinform., 2021)

StructuralVariantAnnotation: a R/Bioconductor foundation for a caller-agnostic structural variant software ecosystem. - Daniel Cameron; Ruining Dong; Anthony T. Papenfuss (Bioinform., 2022)

A systematic review of computational methods for designing efficient guides for CRISPR DNA base editor systems. - Göknur Giner; Saima Ikram; Marco J. Herold; Anthony T. Papenfuss (Briefings Bioinform., 2023)

cellsig plug-in enhances CIBERSORTx signature selection for multidataset transcriptomes with sparse multilevel modelling. - Md. Abdullah-Al-Kamran Khan; Jian Wu; Yuhan Sun; Alexander D. Barrow; Anthony T. Papenfuss; Stefano Mangiola (Bioinform., 2023)