The book of seahtrue
Preface
This is the R Seahorse data analysis manual using functions from the Seahtrue package. Its purpose is to demonstrate and educate how to use R for Extracellular Flux analysis. We use a dedicated data analysis pipeline for quality control and advanced plotting of the data.
You can run R this manual in your browser and do not need to install any R or Rstudio software on your computer.
The manual is targeted to all levels of learning, meaning that also interested learners without any R background or programming knowledge can use it
To turn your .asyr Seahorse Wave file into an excel .xlsx file, you can use the Seahorse Wave desktop software or the Seahorse analytics website from Agilent:
https://seahorseanalytics.agilent.com
Lots of info regarding Seahorse analysis including how it works and how to run experiments is available from the Agilent website
All things lab - How to run an assay:
https://www.agilent.com/en/product/cell-analysis/how-to-run-an-assay
All other Agilent Seahorse info:
https://www.agilent.com/en/products/cell-analysis/how-seahorse-xf-analyzers-work
Resources
Free books
Telling Stories with data
Excellent very complete overview covering basic R coding, communicating science, and statistics. These two chapters are particularly good:
Clean and prepare https://tellingstorieswithdata.com/09-clean_and_prepare.html
appendix 1: R essentials https://tellingstorieswithdata.com/20-r_essentials.html
R for data Science
The go-to book when you want to get familiar with R and tidy from Hadley Wickham and others from Posit https://r4ds.hadley.nz/
Nice sections, for example:
ggplot basics https://r4ds.hadley.nz/data-visualize
lubridate date and time basics https://r4ds.hadley.nz/datetimes
Functional programming book
Nice visualizations of data structures and operations
vectors, lists, tibbles https://dcl-prog.stanford.edu/data-structure-basics.html
map and purrr https://dcl-prog.stanford.edu/purrr-basics.html
Fundamentals of Data Visualization
Everything you want to know about visualizing data using ggplot, with beautifull plots. Also, all code fully available on github
associations (scatter plots etc) https://clauswilke.com/dataviz/visualizing-associations.html
uncertainty (error bars and distirbutions etc) https://clauswilke.com/dataviz/visualizing-uncertainty.html
ggplot tutorial by Cedric Scherer https://www.cedricscherer.com/2019/08/05/a-ggplot2-tutorial-for-beautiful-plotting-in-r/
Webr/WASM
webr REPL - a full complete rstudio-like R environment in the browser https://webr.r-wasm.org/latest/
Webr/wasm presentation bob rudis - (how I got interested in webr/wasm) - https://www.youtube.com/watch?v=inpwcTUmBDY
Webr manual https://docs.r-wasm.org/webr/latest/
Webr on github https://github.com/r-wasm/webr/
Other info
Learn to purrr, Rebecca Barter - https://www.rebeccabarter.com/blog/2019-08-19_purrr
Movies:
Purrr and map functions explained by Hadley - https://www.youtube.com/watch?v=EGAs7zuRutY
R fun
https://twitter.com/rafamoral/status/1571622591219236864?s=20&t=RJWOSe30-8bbDxgLIamRUQ