flowDensity protocols

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flowDensity statistics

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flowDensity specifications

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Unique identifier OMICS_07033
Name flowDensity
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 1.14.0
Stability Stable
Requirements
methods, stats, gplots, graphics, grDevices, car, flowCore, sp, rgeos, RFOC, flowWorkspace(>=3.20.5)
Maintained Yes

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Publication for flowDensity

flowDensity in pipelines

 (3)
2017
PMCID: 5499741
PMID: 28521011
DOI: 10.1093/nar/gkx430

[…] option. flow cytometry data were exported from the acquisition program (facsdiva) in the fcs3.0 format with a data resolution of 218. a custom r programme was written (using flowcore, flowviz and flowdensity bioconductor packages; see ) to calculate statistics for each file. for calculating the coefficients of variation, cytometry files were processed as follows: the first second, and final […]

2017
PMCID: 5720752
PMID: 29216232
DOI: 10.1371/journal.pone.0188853

[…] an emission filter with bandpass of 530/40. for each sample, 100,000 events were counted at a rate between 1000 and 3000 events per second. data was processed by r (3.2.5) with flowcore, flowviz and flowdensity packages., if indole production is an integral part of the cellular response to heat stress, both tryptophan import and the indole production enzyme (tnaa) must, of necessity, be active […]

2016
PMCID: 5314777
PMID: 27928055
DOI: 10.1093/nar/gkw1194

[…] option. flow cytometry data were exported from the acquisition program (facsdiva) in the fcs3.0 format with a data resolution of 218. a custom r programme was written (using flowcore, flowviz and flowdensity bioconductor packages) to calculate statistics for each file. for calculating the coefficients of variation (cv values), cytometry files were processed as follows: the first second, […]


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flowDensity in publications

 (3)
PMCID: 4748244
PMID: 26861911
DOI: 10.1038/srep20686

[…] was excluded from the analysis because markers in the fcs file were mislabeled and could not be matched to the expected panels., 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 this paper. (see ). […]

PMCID: 4515551
PMID: 26284066
DOI: 10.3389/fimmu.2015.00380

[…] [for example, flowpeaks ()], while others include hierarchical clustering in their combined approach [for example, citrus () and spade ()]., one of the most recently published software packages, flowdensity (), offers a different approach. instead of using clustering or model-based approaches to identify cellular populations, the software employs a manual gating strategy. this approach […]

PMCID: 4183538
PMID: 25275464
DOI: 10.1371/journal.pone.0108481

[…] with a high-throughput sampler (bd biosciences, nj, usa). t-regs were analyzed using flowjo 9.6 (treestar inc, ashland, or). t-cell subset analysis employed an automated gating pipeline using the flowdensity algorithm . this approach uses customized threshold calculations for the different cell subsets to mimic a manual gating scheme based on expert knowledge of hierarchical gating order […]


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flowDensity institution(s)
Terry Fox Laboratory, BC Cancer Agency Research Centre, Vancouver, BC, Canada

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