An R shiny web app for streamlining respirometry analysis in R. Respite loads raw respirometry data, automatically segments it, and allows you to select a stable segment from which produce a trend plot and equation.
Manual rate analysis can be done in Excel, but is time consuming, as you have to follow all of these steps:
- Export from the electrode software as a CSV
- Import the CSV into Excel
- Select a stable range of points, somewhat arbitrarily
- From these, create a trend plot
- Extract the trend line from the plot
Respite automates all these steps, and increases the reproducibility of the method, as it requires of less guesswork.
Alternatively, there exists software for analysing this data.
For example, respR is a promising R package that provides many helpful utilities.
However, using such a package still has the barrier of needing to write R code, while Respite provides a user-friendly web interface.
In addition, respR requires the user to manually determine segments of the data (ie peaks), whereas Respite does this automatically.
Most users will be able to access the application at https://multimeric.shinyapps.io/Respite/. The application itself contains help that explains how to use it, but if you have any further questions please create an issue at https://github.com/GreeningLab/Respite/issues. If this server is overloaded or you want to make manual adjustments, please read on to the next section.
In the terminal (e.g. bash):
git clone https://github.com/GreeningLab/Respite.git
cd RespiteThen, in an R console:
# Install dependencies
install.packages('renv')
renv::restore()
# Run application
shiny::runApp()Respite still has many possible extensions.
In particular, it only supports .ulog logging files.
If you would like to contribute a new logging parser, please file an issue at https://github.com/GreeningLab/Respite/issues and we can discuss how this might be done.
Thank you particularly to Associate Professor Rebecca Killick, whose changepoint and EnvCpt packages this relies heavily on.