gcplyr was created to make it easier to import, wrangle, and do model-free analyses of microbial growth curve data, as commonly output by plate readers.
gcplyrcan flexibly import all the common data formats output by plate readers and reshape them into ‘tidy’ formats for analyses.
gcplyrcan import experimental designs from files or directly in
R, then merge this design information with density data.
- This merged tidy-shaped data is then easy to work with and plot using functions from
gcplyrand popular packages
gcplyrcan calculate plain and per-capita derivatives of density data.
gcplyrhas several methods to deal with noise in density or derivatives data.
gcplyrcan extract parameters like growth rate/doubling time, carrying capacity, diauxic shifts, extinction, and more without fitting an equation for growth to your data.
Please send all questions, requests, comments, and bugs to mikeblazanin [at] gmail [dot] com
You can install the most recently-released version from GitHub by running the following lines in R:
You can install the version most-recently released on CRAN by running the following line in R:
The best way to get started is to read through the articles series, which breaks down a typical workflow using
gcplyr from start to finish, starting with the introduction:
- Importing and transforming data:
- Incorporating design information:
- Pre-processing and plotting your data:
- Processing your data:
- Analyzing your data:
- Dealing with noise:
- Statistics, merging other data, and other resources:
- Working with multiple plates: