In biology, Fluorescence Dilution (FD) experiments / proliferation assays are used to assess growth and migration at the single-cell level. Mathematical models can be used to extract parameters such as the division, death and migration rates and their variability. This package provides generic functions to manipulate FD data and solve for these parameters. It can be used both in immunology and microbiology.
Full documentation is available here. An example workflow can be found here and a performance benchmark here. Details are in our upcoming article (Chauvin et al. 2018).
The development version can be installed from github:
if (!require(devtools))
install.packages("devtools")
devtools::install_github("hchauvin/fluodilution", subdir="fluodilution")
# To install all the suggested packages as well:
devtools::install_github("hchauvin/fluodilution",
subdir="fluodilution",
dependencies=TRUE)A release version will be available soon on bioconductor.
The fluodilution package can be consumed either using devtools, bioconductor or
bazel/rules_r, which is a set of
Bazel rules for the R statistical language.
With Bazel, the external dependencies of the project are described in WORKSPACE
and cran. Additional test scripts are available in fdInvariants.
These scripts are run with bazel test and, among other things, test the validity of our
distribution models against agent-based simulations. Because they are more expensive to run
than your usual R package tests, they are not run when R CMD check is invoked.