flowViz statistics

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flowViz specifications

Information


Unique identifier OMICS_05615
Name flowViz
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 1.44.0
Stability Stable
Requirements
methods, stats, RColorBrewer, grid, graphics, Biobase, utils, stats4, grDevices, lattice, knitr, MASS, KernSmooth, R(>=2.7.0), latticeExtra, hexbin, colorspace, flowCore, flowStats, flowCore(>=1.41.9), IDPmisc
Maintained Yes

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Documentation


Publication for flowViz

flowViz in pipelines

 (6)
2017
PMCID: 5352146
PMID: 28257432
DOI: 10.1371/journal.ppat.1006236

[…] temperature. cells were scrapped and data was acquired using bd facsdiva acquisition software in bd facs canto ii flow cytometer (bd). data was analyzed and plotted using r packages flowcore and flowviz., heparinized blood was immediately diluted in 1:1 ratio by volume with dpbs. diluted blood was layered on ficoll-paque (himedia) and centrifuged at 2000 rpm for 45 min. interface containing […]

2017
PMCID: 5499741
PMID: 28521011
DOI: 10.1093/nar/gkx430

[…] the ‘area’ 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, […]

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

[…] through 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, […]

2016
PMCID: 4979487
PMID: 27551515
DOI: 10.1038/cddiscovery.2016.22

[…] 7-aad. the time and staining concentrations of all the fluorescent dyes were performed as per the manufacturer’s directions. the data were analyzed and plotted using the r-packages ‘flowcore’ and ‘flowviz’. for measurement of momp in hypoxia experiments, 2×104 cells were plated per well in a 96-well plate. the staining buffer of jc-1 staining (life technologies corporations) was kept […]

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 (), […]


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flowViz in publications

 (13)
PMCID: 5908957
PMID: 29706940
DOI: 10.3389/fmicb.2018.00719

[…] ()., in general at least 5000 events were collected for data analysis, with only a limited number of exceptions. flow cytometric data were analyzed with the flowcore-package and visualized by flowviz-package of r-software. prior to analysis data were bi-exponentially transformed., the accumulation of enzymatic resistant empty cell walls was measured with an imagestream®x mk ii flow […]

PMCID: 5919758
PMID: 29620524
DOI: 10.7554/eLife.31867.052

[…] the fortessa, with signals recorded for forward and side scatter, mruby (using the texas red laser/filter set), and gfp (using the fitc laser/filter set)., data were analyzed using the flowcore and flowviz modules of r (; ). beads and cells were first identified based on their forward scatter and side scatter (fsc/ssc) values (using permissive gates that capture the vast majority […]

PMCID: 5352146
PMID: 28257432
DOI: 10.1371/journal.ppat.1006236

[…] temperature. cells were scrapped and data was acquired using bd facsdiva acquisition software in bd facs canto ii flow cytometer (bd). data was analyzed and plotted using r packages flowcore and flowviz., heparinized blood was immediately diluted in 1:1 ratio by volume with dpbs. diluted blood was layered on ficoll-paque (himedia) and centrifuged at 2000 rpm for 45 min. interface containing […]

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 (), […]

PMCID: 4888886
PMID: 27303742
DOI: 10.1128/mSphere.00101-16

[…] sorting and iga-coated-cell sorting), as described for . each tube finally contained 540,000 facs-separated cells (). the proportion of cells in bacterial fractions was calculated using the “flowviz” package from the r statistics environment., dna from all the 96 samples (active-f, inactive-f, iga-pos-f, and iga-neg-f fractions for each of the 24 patients) was extracted at one time […]


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flowViz institution(s)
Fred Hutchinson Cancer Research Center, Seattle, WA, USA

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