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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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Maintainer


  • person_outline Raphael Gottardo <>

Publication for OpenCyto

OpenCyto in publications

 (5)
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., cytokines measurement of culture supernatants was performed using the human th1/th2 10-plex tissue culture kit from msd platform. supernatants of 96-well culture […]

PMCID: 5572329
PMID: 28878775
DOI: 10.3389/fimmu.2017.01008

[…] 9.9 tree star). gating strategies for both panels are shown in figures s1 and s2 in supplementary material., 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 […]

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., mice (n = 8– […]

PMCID: 4748244
PMID: 26861911
DOI: 10.1038/srep20686

[…] methods for this task, we leveraged the flowcap project to compare and select the best performing algorithms based on a pilot dataset. the best-performing algorithms were combined using the opencyto framework to leverage the best features of each, and compared to a central manual analysis in terms of variability and bias on four staining panels using both lyophilized and cryopreserved […]

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

[…] integrated approach combining targeted feature extraction with dimension reduction can be used to identify and visualize biological differences in rare, antigen‐specific cell populations. by using opencyto to perform semi‐automated gating and features extraction of flow cytometry data, followed by dimensionality reduction with t‐sne we are able to identify polyfunctional subpopulations […]


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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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