GenePattern flow cytometry suite

Source Code for Biology and Medicine
Josef SpidlenRyan Brinkman

Abstract

Traditional flow cytometry data analysis is largely based on interactive and time consuming analysis of series two dimensional representations of up to 20 dimensional data. Recent technological advances have increased the amount of data generated by the technology and outpaced the development of data analysis approaches. While there are advanced tools available, including many R/BioConductor packages, these are only accessible programmatically and therefore out of reach for most experimentalists. GenePattern is a powerful genomic analysis platform with over 200 tools for analysis of gene expression, proteomics, and other data. A web-based interface provides easy access to these tools and allows the creation of automated analysis pipelines enabling reproducible research. In order to bring advanced flow cytometry data analysis tools to experimentalists without programmatic skills, we developed the GenePattern Flow Cytometry Suite. It contains 34 open source GenePattern flow cytometry modules covering methods from basic processing of flow cytometry standard (i.e., FCS) files to advanced algorithms for automated identification of cell populations, normalization and quality assessment. Internally, these modules leverage from functio...Continue Reading

References

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Citations

Aug 15, 2015·Cytometry. Part a : the Journal of the International Society for Analytical Cytology·Chiaowen HsiaoRichard H Scheuermann
Apr 25, 2015·Cytometry. Part a : the Journal of the International Society for Analytical Cytology·Lin LinRaphael Gottardo
Mar 19, 2016·Cytometry. Part a : the Journal of the International Society for Analytical Cytology·Kipper Fletez-BrantPratip K Chattopadhyay
Apr 10, 2016·Cytometry. Part a : the Journal of the International Society for Analytical Cytology·F Gondois-ReyD Olive
May 17, 2015·Methods : a Companion to Methods in Enzymology·Kirsten E DigginsJonathan M Irish
Apr 23, 2015·Immunity·Pia KvistborgCedrik M Britten
Apr 25, 2017·Expert Review of Vaccines·Richard H ScheuermannWayne C Koff
Oct 13, 2017·European Journal of Immunology·Andrea CossarizzaJakob Zimmermann
Oct 22, 2019·European Journal of Immunology·Andrea CossarizzaArturo Zychlinsky

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Methods Mentioned

BETA
FCS
Flow Cytometry
Feature extraction

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