Package: ceas 1.0.0
Rachel House
ceas: Cellular Energetics Analysis Software
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) <doi:10.1074/jbc.m116.774471>.
Authors:
ceas_1.0.0.tar.gz
ceas_1.0.0.zip(r-4.5)ceas_1.0.0.zip(r-4.4)ceas_1.0.0.zip(r-4.3)
ceas_1.0.0.tgz(r-4.4-any)ceas_1.0.0.tgz(r-4.3-any)
ceas_1.0.0.tar.gz(r-4.5-noble)ceas_1.0.0.tar.gz(r-4.4-noble)
ceas_1.0.0.tgz(r-4.4-emscripten)ceas_1.0.0.tgz(r-4.3-emscripten)
ceas.pdf |ceas.html✨
ceas/json (API)
NEWS
| # Install 'ceas' in R: |
| install.packages('ceas', repos = c('https://jamespeapen.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/jamespeapen/ceas/issues
Last updated 3 months agofrom:2d48eaddd3. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 17 2024 |
| R-4.5-win | OK | Nov 17 2024 |
| R-4.5-linux | OK | Nov 17 2024 |
| R-4.4-win | OK | Nov 17 2024 |
| R-4.4-mac | OK | Nov 17 2024 |
| R-4.3-win | OK | Nov 17 2024 |
| R-4.3-mac | OK | Nov 17 2024 |
Exports:atp_plotbioscope_plotget_energeticsget_energetics_summaryget_rate_summarymake_bioscope_plotnormalizepartition_datarate_plotread_data
Dependencies:cellrangerclicolorspacecpp11crayondata.tablefansifarverggplot2gluegtablehmsisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigprettyunitsprogressR6RColorBrewerreadxlrematchrlangscalestibbleutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| ATP Plot | atp_plot |
| Bioenergetic Scope Plot | bioscope_plot |
| Calculate ATP Production from OXPHOS and Glycolysis | get_energetics |
| Calculate ATP Production Mean and Standard Deviation | get_energetics_summary |
| Rates summary | get_rate_summary |
| Bioenergetic Scope Plot Shortcut | make_bioscope_plot |
| Normalize Seahorse data | normalize |
| Organize Seahorse Data | partition_data |
| Rate plot | rate_plot |
| Read Seahorse Wave Excel File | read_data |