flowCore protocols

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flowCore specifications

Information


Unique identifier OMICS_05596
Name flowCore
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 1.46.2
Stability Stable
Requirements
R(>=2.10.0), methods, stats, graphics, Biobase, utils, testthat, stats4, Rcpp, knitr, corpcor, matrixStats, graph, Rgraphviz, gridExtra, rrcov, flowViz, flowWorkspace, flowWorkspaceData, BiocGenerics(>=0.1.14), flowStats, openCyto, ggcyto
Maintained Yes

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  • person_outline Mike Jiang <>

Publication for flowCore

flowCore in pipelines

 (7)
2017
PMCID: 5352146
PMID: 28257432
DOI: 10.1371/journal.ppat.1006236

[…] minutes at room 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. […]

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

[…] using 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: […]

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

[…] and measured 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, […]

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

[…] and 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) […]

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

[…] correspondence (, , ), 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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flowCore in publications

 (96)
PMCID: 5953949
PMID: 29765016
DOI: 10.1038/s41467-018-04234-4

[…] analysis was conducted on a becton dickinson (bd) lsrii, and fcs files were exported using facsdiva (v6.2). analysis of flow cytometric data was conducted in r/bioconductor (v.3.2.2) using the “flowcore” (v.1.36.9) package or flowjo software (v9.7.6). validation data for all antibodies used are available on the manufacturer’s website., for bone marrow cells cd45.2+ dnmt3-sufficient […]

PMCID: 5915400
PMID: 29691402
DOI: 10.1038/s41467-018-04054-6

[…] between isogenic lines with and without marker (ebc5 vs. ebc47, ebc37 vs. ebc59, etc.) to measure the potential marker effect in each background. measurements were analysed in r using the package flowcore. due to unequal variance among groups, statistical significance was measured using a kruskal–wallis test with a dunn’s post hoc test for significance., we calculated the selection […]

PMCID: 5908957
PMID: 29706940
DOI: 10.3389/fmicb.2018.00719

[…] to their different pigmentation pattern ()., 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 […]

PMCID: 5900032
PMID: 29686665
DOI: 10.3389/fimmu.2018.00486

[…] (www.cytobank.org; cytobank inc.) or in r. biaxial gating was performed on flowjo version 10 software (treestar)., fetal calf serum files were imported into r via the read.fcs function in the flowcore package, as described previously (). t-sne analysis was performed using custom r scripts using r packages that perform the barnes-hut implementation of t-sne. cells from each cluster […]

PMCID: 5889640
PMID: 29563231
DOI: 10.1073/pnas.1717474115

[…] in sorting experiments, ml216-treated or control 6-tgr and -tgs population were recovered for sequencing. for quantification, we performed post hoc analysis using the r bioconductor package flowcore (), principally by clustering using the forward scatter area and dapi/pacific blue-a channels into live and dead clusters using mclust (version 5.2) (, ) in 6-tg–treated experiments, […]


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flowCore institution(s)
Life Sciences Department, Computational Biology Program, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; EA SeRAIC INSERM, IRISA – Symbiose, Université de Rennes, Rennes, France; Terry Fox Laboratory, British Columbia Cancer Agency Research Centre, Vancouver, BC, Canada; AdBrite Inc, San Francisco, CA, USA; BD Biosciences, Research Triangle Park, NC, USA
flowCore funding source(s)
This work was supported by NIH grant EB005034, NIH grant R01 EB008400, and the Michael Smith Foundation for Health Research.

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