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flowCore specifications


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
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




No version available



  • person_outline Mike Jiang

Publication for flowCore

flowCore citations


Genetic mapping of species differences via in vitro crosses in mouse embryonic stem cells

Proc Natl Acad Sci U S A
PMCID: 5889640
PMID: 29563231
DOI: 10.1073/pnas.1717474115

[…] ulations. 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, consider […]


Genomics of cellular proliferation in periodic environmental fluctuations

Mol Syst Biol
PMCID: 5836541
PMID: 29507053
DOI: 10.15252/msb.20177823

[…] Raw .fcs files were analysed using the flowCore package (version 1.34.3) from Bioconductor (Hahne et al, ) and custom codes. Cells of homogeneous size were dynamically gated as follows: (i) removal of samples containing < 2,000 cells, (ii) […]


Assigning function to natural allelic variation via dynamic modeling of gene network induction

Mol Syst Biol
PMCID: 5787706
PMID: 29335276
DOI: 10.15252/msb.20177803

[…] cord 10,000 cells per sample. Each set of data is representative of the results of two independent experiments (each comprising three technical replicates).Flow cytometry data were analyzed using the flowCore package from Bioconductor (Hahne et al, ). Cells of homogeneous size were dynamically gated as follows: (i) removal of events with saturated signals (FSC, SSC, or FL1 = 1023 or = 0), (ii) cor […]


Cytochemical flow analysis of intracellular G6PD and aggregate analysis of mosaic G6PD expression

PMCID: 5888147
PMID: 29240263
DOI: 10.1111/ejh.13013

[…] al software “R” (http://www.r-project.org/) (R Foundation for statistical computing, Vienna, Austria). Custom scripts were written to generate the algorithm and GUI as well as implementation of the R flowCore package in R for the importation of flow cytometry data as well as R shiny package for building the graphical user interface. The flowCore package was developed at Bioconductor (WA, USA). Shi […]


Three distinct developmental pathways for adaptive and two IFN γ producing γδ T subsets in adult thymus

Nat Commun
PMCID: 5715069
PMID: 29203769
DOI: 10.1038/s41467-017-01963-w

[…] Equal numbers of γδ T cells were down-sampled from each replicate, concatenated to a single fcs file using FlowJo and used for analysis in R using the 'flowCore' and 'cytofkit' packages, . t-SNE was calculated for 10,000 cells based on the expression of CD24, CD25, CD73, CD117, CD200 and CD371. Due to the stochasticity of the algorithm, multiple t-SN […]


Avocado fruit maturation and ripening: dynamics of aliphatic acetogenins and lipidomic profiles from mesocarp, idioblasts and seed

BMC Plant Biol
PMCID: 5623960
PMID: 28969589
DOI: 10.1186/s12870-017-1103-6

[…] ffice Professional Plus 2013) “Add Trendline” function. Contents mentioned in the text are shown as mean and standard deviation unless otherwise stated. Flow cytometry data was accessed by use of the flowCore library [], and purity assessed by predictive Linear Discriminant Analysis (pLDA) with the DiscriMiner library []. Direct access to MS files was achieved through ncdf package [], and generati […]


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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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