flowClust protocols

flowClust statistics

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Associated diseases

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flowClust specifications

Information


Unique identifier OMICS_05595
Name flowClust
Software type Package/Module
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 3.18.0
Stability Stable
Requirements
methods, BiocGenerics, Biobase, testthat, ellipse, graph, RBGL, R(>=2.5.0), flowCore, flowViz, MCMCpack, clue, mnormt, flowWorkspace, flowWorkspaceData
Maintained Yes

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Documentation


Publication for flowClust

flowClust in pipeline

2016
PMCID: 5005935
PMID: 27630823
DOI: 10.3389/fonc.2016.00188

[…] , ), and (5) categorizing samples into distinct classes and identifying phenotypes (, , ). a number of open-source r packages have been developed to solve different steps, such as flowcore, flowviz, flowclust, flowtrans, flowstats, and flowtype packages in bioconductor (). several other web-based platforms are also available for automated fc data analysis, such as immport (), genepattern (), […]


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flowClust in publications

 (12)
PMCID: 5300971
PMID: 28239376
DOI: 10.3389/fimmu.2017.00054

[…] to automated gating. dc’s were defined as cd3−cd14−cd19−cd56−cd16−hla-dr+live cells. in the dc gate, the pdc were gated as cd33lowbdca2+cd123+ cells, the mdc as cd33highbdca2−cd123− cells., the flowclust implementation version 3.4.11on r version 3.1.2 under linux cent os 6 was applied on the following parameters: cd56-pc7, cd16-apch7, nkg2a-pacblue, nkg2c-pe, cd57-fitc, to compute clusters […]

PMCID: 5179518
PMID: 28066414
DOI: 10.3389/fimmu.2016.00603

[…] following settings: maximum number of iterations = 10,000, perplexity = 258 (that is 10% of the total number of data points), theta = 0 (exact t-sne)., model-based clustering was performed using the flowclust (, ) r package with the following settings: gaussian mixture models were used (ν = ∞), convergence tolerance of expectation-maximization (em) = 10−15, maximum number of em iterations = 10 […]

PMCID: 5005935
PMID: 27630823
DOI: 10.3389/fonc.2016.00188

[…] , ), and (5) categorizing samples into distinct classes and identifying phenotypes (, , ). a number of open-source r packages have been developed to solve different steps, such as flowcore, flowviz, flowclust, flowtrans, flowstats, and flowtype packages in bioconductor (). several other web-based platforms are also available for automated fc data analysis, such as immport (), genepattern (), […]

PMCID: 4635854
PMID: 26594214
DOI: 10.3389/fimmu.2015.00564

[…] new tools are then required to address these problems. recently, algorithms for automatic gating and 2d mapping of high dimensional dataset have been developed, such as spade (), visne (), flowclust (), or flock (, ). these algorithms combined to classification methods enable the visualization of multiple parameters and summarize information. these approaches are of particular […]

PMCID: 4455047
PMID: 25778704
DOI: 10.1038/nature14244

[…] of yfp. data were collected from fl1 using a 533/30 nm filter. each culture was sampled for 2–3 seconds, resulting in approximately 20,000 recorded events., samples were processed using the flowclust and flowcore packages within r (v 3.0.2) and custom r scripts (). raw data () was log10 transformed and artifacts were removed by excluding events with extreme fsc.h, fsc.a, ssc.h, ssc.a […]


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flowClust institution(s)
Department of Statistics, University of British Columbia, Vancouver, BC, Canada

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