Dithionite Scramblase Assay Analysis

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'.


An R package for the automated analysis of dithionite scramblase assays.

To install the development version, you first need the devtools package.

install.packages("devtools")

Then you can install the flippant package using

library(devtools)
install_bitbucket("jog2030/flippant")

A stable version is planned to be made available via Bioconductor.

The manuscript

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 dataset

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.

Functions

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.

News

Reference manual

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install.packages("flippant")

1.1.0 by Johannes Graumann, 6 months ago


Browse source code at https://github.com/cran/flippant


Authors: Johannes Graumann [cre, aut], Richard Cotton [ctb]


Documentation:   PDF Manual  


GPL (>= 3) license


Imports assertive.files, assertive.numbers, assertive.properties, assertive.strings, assertive.types, data.table, magrittr, minpack.lm, plyr, RcppRoll, stringi, utils, withr, wmtsa

Depends on ggplot2

Suggests bookdown, devtools, microbenchmark, multipanelfigure, pander, roxygen2, tools


See at CRAN