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CytoSPADE: high-performance analysis and visualization of high-dimensional cytometry data

M. D. Linderman, Z. Bjornson, E. F. Simonds, P. Qiu, R. V. Bruggner, K. Sheode, T. H. Meng, S. K. Plevritis, G. P. Nolan
2012 Bioinformatics  
CytoSPADE is a high-performance implementation of an interface for the Spanning-tree Progression Analysis of Density-normalized Events algorithm for tree-based analysis and visualization of this high-dimensional  ...  cytometry data.  ...  high-dimensional mass cytometry datasets with millions of cells.  ... 
doi:10.1093/bioinformatics/bts425 pmid:22782546 pmcid:PMC3436846 fatcat:7mvtgwp3vbe5lnzpl2ct62suve

Methods for discovery and characterization of cell subsets in high dimensional mass cytometry data

Kirsten E. Diggins, P. Brent Ferrell, Jonathan M. Irish
2015 Methods  
Here, we introduce a workflow for high dimensional mass cytometry data that emphasizes unsupervised approaches and visualizes data in both single cell and population level views.  ...  The flood of high-dimensional data resulting from mass cytometry experiments that measure more than 40 features of individual cells has stimulated creation of new single cell computational biology tools  ...  Event restriction is traditionally performed using biaxial gating (Table 1) , but given the high dimensionality of mass cytometry data, use of viSNE ( Figure 1 ) can simplify the process of distinguishing  ... 
doi:10.1016/j.ymeth.2015.05.008 pmid:25979346 pmcid:PMC4468028 fatcat:rw6vce2gfrdz7ft2glr2gkzwbq

Algorithmic Tools for Mining High-Dimensional Cytometry Data

Cariad Chester, Holden T. Maecker
2015 Journal of Immunology  
Conventional data analysis by manual gating of cells in biaxial dot plots is often subjective, time consuming, and neglectful of much of the information contained in a highly dimensional cytometric dataset  ...  The advent of mass cytometry has led to an unprecedented increase in the number of analytes measured in individual cells, thereby increasing the complexity and information content of cytometric data.  ...  Acknowledgments We thank Henrik Mei and Michael Leipold for helpful discussions and editing. Disclosures The authors have no financial conflicts of interest.  ... 
doi:10.4049/jimmunol.1500633 pmid:26188071 pmcid:PMC4507289 fatcat:qqcs6gkrbjdrrafkizwmvopoha

Recent Advances in Computer-Assisted Algorithms for Cell Subtype Identification of Cytometry Data

Peng Liu, Silvia Liu, Yusi Fang, Xiangning Xue, Jian Zou, George Tseng, Liza Konnikova
2020 Frontiers in Cell and Developmental Biology  
The progress in the field of high-dimensional cytometry has greatly increased the number of markers that can be simultaneously analyzed producing datasets with large numbers of parameters.  ...  To overcome this, a large number of automated tools have been developed to aid with cellular clustering of multi-dimensional datasets.  ...  clustering tools for high-dimensional cytometry data analysis.  ... 
doi:10.3389/fcell.2020.00234 pmid:32411698 pmcid:PMC7198724 fatcat:f4ej3ru77fetvad75t5iqz22zy

Identification of cardiovascular lineage descendants at single-cell resolution

G. Li, K. Plonowska, R. Kuppusamy, A. Sturzu, S. M. Wu
2015 Development  
In this study, we aimed to establish a single-cell quantitative PCR platform and perform side-by-side comparison between cardiac progenitor cells (CPCs) and cardiomyocytes (CMs) derived from mESCs and  ...  These results demonstrate that multiplex gene expression analysis in single cells is a powerful tool for examining the unique behaviors of individual embryo-or mESC-derived cardiac cells.  ...  Acknowledgements We thank Sopheak Sim at the Stanford Institute for Stem Cell Biology and Regenerative Medicine for assistance with the Fluidigm Biomark HD array, Drs  ... 
doi:10.1242/dev.116897 pmid:25633351 pmcid:PMC4352984 fatcat:jv2vqhtb7rhyvb74qdl5ysn4ay

Mapping the effects of drugs on the immune system

Brian A Kidd, Aleksandra Wroblewska, Mary R Boland, Judith Agudo, Miriam Merad, Nicholas P Tatonetti, Brian D Brown, Joel T Dudley
2015 Nature Biotechnology  
To our knowledge, systematic integration and analysis of chemogenomic and immunogenomic data have not been performed.  ...  To survey a broader array of immune cell changes following treatment, we performed mass cytometry (CyTOF) using a panel of 19 markers to evaluate cell differences in the spleens of mice treated with clioquinol  ...  Reprints and permissions information is available online at http://www.nature.com/ reprints/index.html. A n A ly s i s npg  ... 
doi:10.1038/nbt.3367 pmid:26619012 pmcid:PMC4706827 fatcat:yh2hf6wb4zcdhpta46lrahlcfy