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Protocols

OpenCyto specifications

Information


Unique identifier OMICS_05591
Name OpenCyto
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 1.13.5
Stability Stable
Requirements
flowWorkspace, flowCore, flowViz, ncdfFlow
Maintained Yes

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Documentation


Maintainer


  • person_outline Raphael Gottardo

Publication for OpenCyto

OpenCyto citations

 (6)
library_books

Sensitive and frequent identification of high avidity neo epitope specific CD8+ T cells in immunotherapy naive ovarian cancer

2018
Nat Commun
PMCID: 5854609
PMID: 29545564
DOI: 10.1038/s41467-018-03301-0

[…] at 45 μL per min. FCS files were concatenated and normalized using the cytobank concatenation tool and matlab normalizer, respectively. Data were processed and analyzed with cytobank and R using the OpenCyto and cytofkit packages. […]

call_split

RTS,S/AS01E Malaria Vaccine Induces Memory and Polyfunctional T Cell Responses in a Pediatric African Phase III Trial

2017
Front Immunol
PMCID: 5572329
PMID: 28878775
DOI: 10.3389/fimmu.2017.01008
call_split See protocol

[…] The raw FCS files and manual gates were imported into the R environment () using the OpenCyto framework () and cell counts for the cell gates of interest were obtained for all stimulations and subjects.For the analysis of the effect of vaccination on the frequencies of cells expressin […]

library_books

CymeR: cytometry analysis using KNIME, docker and R

2016
Bioinformatics
PMCID: 5870801
PMID: 27998935
DOI: 10.1093/bioinformatics/btw707

[…] we currently provide access to Cytofkit (), Destiny (), FlowSOM (), PhenoGraph (), SCAFoLLD (), SPADE (), t-SNE (), VorteX () and Wishbone (), and in the latter case we have provided a simple GUI for OpenCyto (). For almost all CymeR functions, the main output is a new FCS file with new columns corresponding to new dimensions, cluster membership or whatever else is applicable. Thus, one could, for […]

library_books

Impact of the microbial derived short chain fatty acid propionate on host susceptibility to bacterial and fungal infections in vivo

2016
Sci Rep
PMCID: 5126587
PMID: 27897220
DOI: 10.1038/srep37944

[…] e pump at 45 μl/min. FCS files were concatenated and normalized using the cytobank concatenation tool and matlab normalizer respectively. Data was processed and analyzed with cytobank and R using the OpenCyto and cytofkit packages. Dimensionality reduction with t-SNE was performed on a merged dataset, consisting of a random selection of 10’000 non granulocyte events from each sample. […]

call_split

Standardizing Flow Cytometry Immunophenotyping Analysis from the Human ImmunoPhenotyping Consortium

2016
Sci Rep
PMCID: 4748244
PMID: 26861911
DOI: 10.1038/srep20686
call_split See protocol

[…] The two top performing gating algorithms - OpenCyto (v. 1.7.4), flowDensity (v. 1.4.0) - in a study run by the FlowCAP consortium aimed at selecting the best performing algorithms for this larger study were chosen for the analysis presented in […]

library_books

Identification and visualization of multidimensional antigen‐specific T‐cell populations in polychromatic cytometry data

2015
Cytometry
PMCID: 4482785
PMID: 25908275
DOI: 10.1002/cyto.a.22623

[…] ents that can be processed by the t‐SNE algorithm within a reasonable amount of time and memory. We have also showed that extracting Ag‐specific T cells helps t‐SNE for visualizing rare cell subsets. OpenCyto provides a convenient and unified platform for gating relevant events, and performing subsequent dimension reduction and visualization. Controlling for constant background in non‐stimulated s […]

Citations

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OpenCyto institution(s)
Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Agency for Science Technology and Research, Singapore Immunology Network, Singapore; Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA; Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA; The Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA; Infectious Diseases Division, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA; Department of Laboratory Medicine, University of Washington, Seattle, WA, USA; Department of Statistics, University of Washington, Seattle, WA, USA
OpenCyto funding source(s)
Supported by NIH grants [R01 EB008400], and grants [UM1 AI068635] and [UM1 AI068618] to the HIV Vaccine Trials Network (HVTN) and the Statistical Data Management Center (SDMC), the Human Immunology Project Consortium (HIPC) [U19 AI089986], and the Collaboration for AIDS Vaccine Discovery [OPP1032325].

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