Enhanced flowType/RchyOptimyx: a BioConductor pipeline for discovery in high-dimensional cytometry data

Kieran O'Neill; Adrin Jalali; Nima Aghaeepour; Holger Hoos; Ryan R Brinkman

doi:10.1093/bioinformatics/btt770

Enhanced flowType/RchyOptimyx: a BioConductor pipeline for discovery in high-dimensional cytometry data

Bioinformatics. 2014 May 1;30(9):1329-30. doi: 10.1093/bioinformatics/btt770. Epub 2014 Jan 8.

Authors

Kieran O'Neill¹, Adrin Jalali, Nima Aghaeepour, Holger Hoos, Ryan R Brinkman

Affiliation

¹ Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada, Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC V6T 1Z3, Canada, Max-Planck-Institut fur Informatik, Saarland University, 66123, Saarbrucken, Germany, Departments of Computer Science and Departments of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.

Abstract

We present a significantly improved version of the flowType and RchyOptimyx BioConductor-based pipeline that is both 14 times faster and can accommodate multiple levels of biomarker expression for up to 96 markers. With these improvements, the pipeline is positioned to be an integral part of data analysis for high-throughput experiments on high-dimensional single-cell assay platforms, including flow cytometry, mass cytometry and single-cell RT-qPCR.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Antigens, CD / analysis
Biomarkers / analysis
Flow Cytometry / methods*
Software

Substances

Antigens, CD
Biomarkers

Abstract

Publication types

MeSH terms

Substances

Grants and funding