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Protocols

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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No version available

Documentation


Publication for flowClust

flowClust citations

 (12)
library_books

A Mature NK Profile at the Time of HIV Primary Infection Is Associated with an Early Response to cART

2017
Front Immunol
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 […]

library_books

TGF β Affects the Differentiation of Human GM CSF+ CD4+ T Cells in an Activation and Sodium Dependent Manner

2016
Front Immunol
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 […]

library_books

Immunophenotype Discovery, Hierarchical Organization, and Template Based Classification of Flow Cytometry Samples

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 (), […]

library_books

Increased NK Cell Maturation in Patients with Acute Myeloid Leukemia

2015
Front Immunol
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 […]

library_books

Selection on noise constrains variation in a eukaryotic promoter

2015
Nature
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 […]

library_books

The structural code of cyanobacterial genomes

2014
Nucleic Acids Res
PMCID: 4132750
PMID: 25056315
DOI: 10.1093/nar/gku641

[…] the highest frequency component was removed, accounting for measurement noise without data normalization. the remaining 5 dft components where then clustered by the model-based clustering tool flowclust (), choosing cluster number k = 10 and assigning all genes annotated but absent from the microarray to cluster 11. the supercoiling-sensitive gene cohorts were taken without […]


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

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