README.md

In ocbe-uio/cellmigRation: Track Cells, Analyze Cell Trajectories and Compute Migration Statistics

cellmigRation

An R package for tracking cells and analyzing their trajectories.

Installation

cellmigRation is under active development and a stable version is yet to be released. However, you can install the current development version of cellmigRation from GitHub with:

# install.packages("remotes")
remotes::install_github("ocbe-uio/cellmigRation")

Example

Example usage:

library(cellmigRation)
#> Loading required package: foreach

data(TrajectoryDataset)
df <- CellMig(TrajectoryDataset[1:100, ])
preproc <- rmPreProcessing(df, PixelSize = 1.24, TimeInterval = 100)
#> This dataset contains: 1 cell(s) in total
#> This dataset contains: 1 cell(s) with more than three steps in their tracks
#> The minimum number of steps:  100 
#> The maximum number of steps:  100 
#> Number of cells with a total number of steps less than  100 steps : 0 
#> All the tracks are adjusted to have only  100  steps

Shiny application

Some cellmigRation features are also available as a standalone web application powered by an R package called Shiny. The Shiny app is still under construction, so it is not feature-complete and is not guaranteed to perform as expected. Until release, we advise you to use the R package directly.

To access the cellmigRation Shiny app, visit https://ocbe.shinyapps.io/cellmigRation/.

Alternatively, you can run the Shiny app locally on your computer. To do so, download a copy of this repository and either run make runshiny or R -e "shiny::runApp('Shinyapp', port=3029)" from its root directory.

Statistics for developers

ocbe-uio/cellmigRation documentation built on Dec. 16, 2021, 10:59 p.m.