Cellular Energetics Analysis Software • ceas

Cellular Energetics Analysis Software

Description

Analysis and visualization of cellular energetics data from Agilent Seahorse XF96. Cellular energetics is how cells make, use, and distribute units of energy (primarily ATP). Measuring real-time cellular energetics is essential to understanding a tissue or cell’s bioenergetic state and fuel dependencies. The Seahorse machine measures a cell’s or matrix’s oxygen consumption rate (OCR) – a proxy of oxidative phosphorylation – and extracellular acidification rate – a proxy of glycolysis. This package offers flexible and fast analysis and plotting capabilities for such data using the methods described by Mookerjee et al. (2017).

Pronunciation

‘ceas’ is pronounced like the word ‘seas’ (siːz, SEEZ).

Installation

CRAN

install.packages("ceas")

Github

You can install the release or development versions from GitHub by cloning the repo. The code on the main branch is in sync with the CRAN releases while the dev branch has the latest updates. Documentation for the dev branch can be found on the dev page of the website (/dev).

git clone https://github.com/jamespeapen/ceas/
git clone -b dev https://github.com/jamespeapen/ceas/ # dev version
R CMD INSTALL ceas

You can also use the R devtools package:

devtools::install_github("jamespeapen/ceas")
devtools::install_github("jamespeapen/ceas", ref = "dev") # dev version

or pak:

pak::pkg_install("jamespeapen/ceas")
pak::pkg_install("jamespeapen/ceas@dev") # dev version

Usage

A user guide is available on the package website. Bug reports may be submitted through GitHub issues.

Contributing

Submit patches using GitHub pull requests or by sending a patch file to james.eapen@vai.org. We follow the tidyverse style guide using styler and lintr.