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Literature DB >> 22782546

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

Michael D Linderman¹, Zach Bjornson, Erin F Simonds, Peng Qiu, Robert V Bruggner, Ketaki Sheode, Teresa H Meng, Sylvia K Plevritis, Garry P Nolan.

Abstract

MOTIVATION: Recent advances in flow cytometry enable simultaneous single-cell measurement of 30+ surface and intracellular proteins. 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. AVAILABILITY: Source code and binaries are freely available at http://cytospade.org and via Bioconductor version 2.10 onwards for Linux, OSX and Windows. CytoSPADE is implemented in R, C++ and Java. CONTACT: michael.linderman@mssm.edu SUPPLEMENTARY INFORMATION: Additional documentation available at http://cytospade.org.

Mesh：

Year: 2012 PMID： 22782546 PMCID： PMC3436846 DOI： 10.1093/bioinformatics/bts425

Source DB: PubMed Journal: Bioinformatics ISSN： 1367-4803 Impact factor: 6.937

6 in total

1. Integration of biological networks and gene expression data using Cytoscape.

Authors: Melissa S Cline; Michael Smoot; Ethan Cerami; Allan Kuchinsky; Nerius Landys; Chris Workman; Rowan Christmas; Iliana Avila-Campilo; Michael Creech; Benjamin Gross; Kristina Hanspers; Ruth Isserlin; Ryan Kelley; Sarah Killcoyne; Samad Lotia; Steven Maere; John Morris; Keiichiro Ono; Vuk Pavlovic; Alexander R Pico; Aditya Vailaya; Peng-Liang Wang; Annette Adler; Bruce R Conklin; Leroy Hood; Martin Kuiper; Chris Sander; Ilya Schmulevich; Benno Schwikowski; Guy J Warner; Trey Ideker; Gary D Bader
Journal: Nat Protoc Date: 2007 Impact factor: 13.491

2. Web-based analysis and publication of flow cytometry experiments.

Authors: Nikesh Kotecha; Peter O Krutzik; Jonathan M Irish
Journal: Curr Protoc Cytom Date: 2010-07

3. Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum.

Authors: Sean C Bendall; Erin F Simonds; Peng Qiu; El-ad D Amir; Peter O Krutzik; Rachel Finck; Robert V Bruggner; Rachel Melamed; Angelica Trejo; Olga I Ornatsky; Robert S Balderas; Sylvia K Plevritis; Karen Sachs; Dana Pe'er; Scott D Tanner; Garry P Nolan
Journal: Science Date: 2011-05-06 Impact factor: 47.728

4. Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE.

Authors: Peng Qiu; Erin F Simonds; Sean C Bendall; Kenneth D Gibbs; Robert V Bruggner; Michael D Linderman; Karen Sachs; Garry P Nolan; Sylvia K Plevritis
Journal: Nat Biotechnol Date: 2011-10-02 Impact factor: 54.908

5. flowClust: a Bioconductor package for automated gating of flow cytometry data.

Authors: Kenneth Lo; Florian Hahne; Ryan R Brinkman; Raphael Gottardo
Journal: BMC Bioinformatics Date: 2009-05-14 Impact factor: 3.169

6. flowCore: a Bioconductor package for high throughput flow cytometry.

Authors: Florian Hahne; Nolwenn LeMeur; Ryan R Brinkman; Byron Ellis; Perry Haaland; Deepayan Sarkar; Josef Spidlen; Errol Strain; Robert Gentleman
Journal: BMC Bioinformatics Date: 2009-04-09 Impact factor: 3.169

6 in total

18 in total

Review 1. Single-cell mass cytometry for analysis of immune system functional states.

Authors: Zach B Bjornson; Garry P Nolan; Wendy J Fantl
Journal: Curr Opin Immunol Date: 2013-08-31 Impact factor: 7.486

Review 2. Algorithmic Tools for Mining High-Dimensional Cytometry Data.

Authors: Cariad Chester; Holden T Maecker
Journal: J Immunol Date: 2015-08-01 Impact factor: 5.422

3. Identification of cardiovascular lineage descendants at single-cell resolution.

Authors: Guang Li; Karolina Plonowska; Rajarajan Kuppusamy; Anthony Sturzu; Sean M Wu
Journal: Development Date: 2015-01-29 Impact factor: 6.868

4. Visualization and cellular hierarchy inference of single-cell data using SPADE.

Authors: Benedict Anchang; Tom D P Hart; Sean C Bendall; Peng Qiu; Zach Bjornson; Michael Linderman; Garry P Nolan; Sylvia K Plevritis
Journal: Nat Protoc Date: 2016-06-16 Impact factor: 13.491

5. Human B-cell and progenitor stages as determined by probability state modeling of multidimensional cytometry data.

Authors: C Bruce Bagwell; Beth L Hill; Brent L Wood; Paul K Wallace; Muaz Alrazzak; Abigail S Kelliher; Frederic I Preffer
Journal: Cytometry B Clin Cytom Date: 2015-05-23 Impact factor: 3.058

6. A continuous molecular roadmap to iPSC reprogramming through progression analysis of single-cell mass cytometry.

Authors: Eli R Zunder; Ernesto Lujan; Yury Goltsev; Marius Wernig; Garry P Nolan
Journal: Cell Stem Cell Date: 2015-03-05 Impact factor: 24.633

7. Statistical classification of multivariate flow cytometry data analyzed by manual gating: stem, progenitor, and epithelial marker expression in nonsmall cell lung cancer and normal lung.

Authors: Daniel P Normolle; Vera S Donnenberg; Albert D Donnenberg
Journal: Cytometry A Date: 2012-12-13 Impact factor: 4.355

8. Toward deterministic and semiautomated SPADE analysis.

Authors: Peng Qiu
Journal: Cytometry A Date: 2017-02-24 Impact factor: 4.355

Review 9. Mass cytometry as a platform for the discovery of cellular biomarkers to guide effective rheumatic disease therapy.

Authors: Nitya Nair; Henrik E Mei; Shih-Yu Chen; Matthew Hale; Garry P Nolan; Holden T Maecker; Mark Genovese; C Garrison Fathman; Chan C Whiting
Journal: Arthritis Res Ther Date: 2015-05-18 Impact factor: 5.156

10. Early reprogramming regulators identified by prospective isolation and mass cytometry.

Authors: Ernesto Lujan; Eli R Zunder; Yi Han Ng; Isabel N Goronzy; Garry P Nolan; Marius Wernig
Journal: Nature Date: 2015-04-01 Impact factor: 49.962