bioRxivBioinformaticsPreprint
FastPG: Fast clustering of millions of single cells
Tom Bodenheimer, Mahantesh M. HalappanavariD, Stuart R. JefferysiD, Ryan GibsoniD, Siyao LiuiD, Peter J. MuchaiD, Natalie StanleyiD, Joel S. ParkeriD, Sara R. SelitskyiD
Abstract
Current single-cell experiments can produce datasets with millions of cells. Unsupervised clustering can be used to identify cell populations in single-cell analysis but often leads to interminable computation time at this scale. This problem has previously been mitigated by subsampling cells, which greatly reduces accuracy. We built on the graph-based algorithm PhenoGraph and developed FastPG which has the same cell assignment accuracy but is on average 27x faster in our tests. FastPG also has higher cell assignment accuracy than two other fast clustering methods, FlowSOM and PARC. AvailabilityFastPG is available here: https://github.com/sararselitsky/FastPG
- Citations
- 25
Reproducibility ledger
Nobody has reported trying to reproduce this paper yet. Did you replicate an experiment or run the code? Your report saves the next lab a week.
Sign in to file a reproducibility report.
Related papers
- PARC: ultrafast and accurate clustering of phenotypic data of millions of single cells
Shobana V. Stassen, Dickson M. D. Siu, … Kevin K. Tsia·BioinformaticsPeer-reviewed·Jan 16, 2020
- Ultrafast clustering of single-cell flow cytometry data using FlowGrid
Xiaoxin Ye, Joshua W. K. Ho·BMC Systems BiologyPeer-reviewed·Apr 1, 2019
- HGC: fast hierarchical clustering for large-scale single-cell data
Ziheng Zou, Kui Hua, Xuegong Zhang·BioinformaticsPeer-reviewed·Jun 4, 2021
- GPseudoClust: deconvolution of shared pseudo-profiles at single-cell resolution
Magdalena E Strauß, Paul Kirk, … Lorenz Wernisch·BioinformaticsPeer-reviewed·Oct 9, 2019
- SCHNEL: Scalable clustering of high dimensional single-cell data
Tamim Abdelaal, Paul de Raadt, … Ahmed Essam Mahfouz·BioinformaticsPeer-reviewed·Sep 7, 2020
- CosTaL: An Accurate and Scalable Graph-Based Clustering Algorithm for High-Dimensional Single-Cell Data Analysis
Y. Li, J. Nguyen, … E. A. Arriaga·bioRxiv·Nov 10, 2022