cyanoFilter

Cyanobacteria Population Identification for Flow Cytometry

An approach to filter out and/or identify two synechococcus type cyanobacteria cells from all particles measured via flow cytometry. It combines known characteristics of these two cyanobacteria strains (BS4 and BS5) alongside gating techniques developed by Mehrnoush, M. et al. (2015) <doi:10.1093/bioinformatics/btu677> in the 'flowDensity' package to identify and separate these cyanobacteria cells from other cell types. Aside the gating techniques in the 'flowDensity' package, an EM style clustering technique is also developed to identify these cyanobacteria cell populations.

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Description file content

Package
cyanoFilter
Title
Cyanobacteria Population Identification for Flow Cytometry
Version
0.1.1
Maintainer
Oluwafemi Olusoji
Description
An approach to filter out and/or identify two synechococcus type cyanobacteria cells from all particles measured via flow cytometry. It combines known characteristics of these two cyanobacteria strains (BS4 and BS5) alongside gating techniques developed by Mehrnoush, M. et al. (2015) in the 'flowDensity' package to identify and separate these cyanobacteria cells from other cell types. Aside the gating techniques in the 'flowDensity' package, an EM style clustering technique is also developed to identify these cyanobacteria cell populations.
URL
BugReports
https://github.com/fomotis/cyanoFilter/issues
Depends
R(>= 3.4), Biobase(>= 2.40.0)
Imports
flowCore(>= 1.42.3), flowDensity (>= 1.10.0), graphics(>= 3.6.0), grDevices(>= 3.6.0), methods(>= 3.5.1), RColorBrewer(>= 1.1-2), Rdpack(>= 0.11-0), stats(>= 3.6.0), stringr(>= 1.3.1), utils(>= 3.6.0)
RdMacros
Rdpack
License
GPL-3
Encoding
UTF-8
LazyData
true
RoxygenNote
6.1.1
Suggests
dplyr, magrittr, knitr, rmarkdown, tidyr
VignetteBuilder
knitr
NeedsCompilation
no
Packaged
2019-08-08 13:35:48 UTC; lucp9544
Author
Oluwafemi Olusoji [aut, cre], Aerts Marc [ctb], Delaender Frederik [ctb], Neyens Thomas [ctb], Spaak jurg [aut]
Repository
CRAN
Date/Publication
2019-08-09 10:30:06 UTC

install.packages('cyanoFilter')

0.1.1

12 days ago

https://github.com/fomotis/cyanoFilter

Oluwafemi Olusoji

GPL-3

Depends on

R(>= 3.4), Biobase(>= 2.40.0)

Imports

flowCore(>= 1.42.3), flowDensity (>= 1.10.0), graphics(>= 3.6.0), grDevices(>= 3.6.0), methods(>= 3.5.1), RColorBrewer(>= 1.1-2), Rdpack(>= 0.11-0), stats(>= 3.6.0), stringr(>= 1.3.1), utils(>= 3.6.0)

Suggests

dplyr, magrittr, knitr, rmarkdown, tidyr

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