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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

Versioning


No version available

Documentation


Publication for flowViz

flowViz citations

 (18)
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

[…] n 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 with an ImageStream®X Mk II flow cytometer […]

library_books

Stochastic tuning of gene expression enables cellular adaptation in the absence of pre existing regulatory circuitry

2018
eLife
PMCID: 5919758
PMID: 29620524
DOI: 10.7554/eLife.31867.052

[…] on 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 of each populat […]

call_split

Indole at low concentration helps exponentially growing Escherichia coli survive at high temperature

2017
PLoS One
PMCID: 5720752
PMID: 29216232
DOI: 10.1371/journal.pone.0188853
call_split See protocol

[…] ured 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. […]

call_split

Translation initiation events on structured eukaryotic mRNAs generate gene expression noise

2017
Nucleic Acids Res
PMCID: 5499741
PMID: 28521011
DOI: 10.1093/nar/gkx430
call_split See protocol

[…] sing 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, […]

call_split

Alternate splicing of transcripts shape macrophage response to Mycobacterium tuberculosis infection

2017
PLoS Pathog
PMCID: 5352146
PMID: 28257432
DOI: 10.1371/journal.ppat.1006236
call_split See protocol

[…] 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. […]

call_split

Minimum noise production of translation factor eIF4G maps to a mechanistically determined optimal rate control window for protein synthesis

2016
Nucleic Acids Res
PMCID: 5314777
PMID: 27928055
DOI: 10.1093/nar/gkw1194
call_split See protocol

[…] sing 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) to calculate statistics for each file. For calculating the coefficients of variation (CV values), cytometry files were processed as follows: The first se […]

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

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