rcell2 examples

Examples for rcell2 and companion packages, rcell2.cellid and rcell2.magick.

The rcell2 packages provide functions to analyze Cell-ID single-cell cytometry data in a tidy and shiny framework.

It also includes sample images to test out the rcell2 packages, located at inst/extdata.

Installation

From R, run:

if(!require(remotes)){
  # Install the "remotes" package if not found:
  install.packages("remotes")
}

# Install rcell2.examples
remotes::install_github("darksideoftheshmoo/rcell2.examples")

This package has no dependencies for installation.

However, all example Rmd notebooks use the rcell2 packages, and many other packages are required to run all the example notebooks.

It is left to the user to install them as needed.

Example image sets

Example image sets can be found at the inst/extdata/sample_datasets directory.

Once the package has been installed in your system, the path to the images can be found by running the following in R's console:

dir(system.file("extdata/sample_datasets/", package = "rcell2.examples"))

There are simple datasets (single-time) and time-course experiments (with multiple image sets per field of view, taken at different times).

Development notebooks

Example data and analysis notebooks can be found in the examples package: rcell2.examples.

The inst/testings directory holds many rmarkdown notebooks, where we explore different analysis approaches to single cell images and cytometry:

• Spatial distribution of fluorescent signals.
• Pattern detection in time-series.
• Classification examples.
• Cell boundary curvature analysis and alignment.
• ...

Todo

• Cleanup and test all notebooks.