The lipid scrambling activity of protein extracts and purified
scramblases is often determined using a fluorescence-based assay involving
many manual steps. flippant offers an integrated solution for the analysis
and publication-grade graphical presentation of dithionite scramblase
assays, as well as a platform for review, dissemination and extension of the
strategies it employs. The package's name derives from a play on the fact
that lipid scrambling is also sometimes referred to as 'flipping'.
The package is originally published as Cotton, R.J., Ploier, B., Goren,
M.A., Menon, A.K., and Graumann, J. (2017). flippant–An R package for the
automated analysis of fluorescence-based scramblase assays. BMC
Bioinformatics 18, 146.
R package for the automated analysis of dithionite scramblase assays.
To install the development version, you first need the devtools package.
Then you can install the flippant package using
A stable version is planned to be made available via Bioconductor.
The manuscript is provided in
Rmd form in the
inst/manuscript directory. Note that building the manuscript takes around an hour, since it runs the whole analysis.
The original data in contained in a
zip file in the
inst/extdata directory. Each file within the
zip archive is a text file. Lines 4 through to the penultimate line contain tab delimited text data.
scramblase_assay_traces draws time series of relative fluorescence vs. acquisition time, possibly split by experiment.
scramblase_assay_plot draws plots of the probability of at least one flippase vs. the protein to phospholipid ratio.
scramblase_assay_stats calculates the fit constant for each experiment.
scramblase_assay_calculations provides a lower-level overview of model fit details.