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output: github_document
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regenerate README.md by running the following in R:
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# cellmigRation
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
<img src="cell_migration_logo.png" width="50%" alt="cellmigRation">
An R package for tracking cells and analyzing their trajectories.
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# 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](https://github.com/) with:
``` r
# install.packages("remotes")
remotes::install_github("ocbe-uio/cellmigRation")
```
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# Example
Example usage:
```{r example}
library(cellmigRation)
data(TrajectoryDataset)
df <- CellMig(TrajectoryDataset[1:100, ])
preproc <- rmPreProcessing(df, PixelSize = 1.24, TimeInterval = 100)
```
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# 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.
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# Statistics for developers
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[](https://travis-ci.org/ocbe-uio/cellmigRation)
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