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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 citations

 (100)
library_books

B cell activation and plasma cell differentiation are inhibited by de novo DNA methylation

2018
Nat Commun
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 […]

library_books

Repeated evolution of self compatibility for reproductive assurance

2018
Nat Commun
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 […]

library_books

Cell Wall Structure of Coccoid Green Algae as an Important Trade Off Between Biotic Interference Mechanisms and Multidimensional Cell Growth

2018
Front Microbiol
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 […]

library_books

CD161 Defines a Functionally Distinct Subset of Pro Inflammatory Natural Killer Cells

2018
Front Immunol
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 […]

library_books

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

2018
Proc Natl Acad Sci U S A
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, […]

library_books

Genomics of cellular proliferation in periodic environmental fluctuations

2018
Mol Syst Biol
PMCID: 5836541
PMID: 29507053
DOI: 10.15252/msb.20177823

[…] at 4°c before being analysed on a facscalibur flow cytometer (bd biosciences). acquisitions were stored on 10,000 cells at a mean rate of 1,000 cells/s., 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, […]


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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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