R Development Page
Contributed R Packages
Below is a list of all packages provided by project Quantitative Fitness Analysis.
Important note for package binaries: R-Forge provides these binaries only for the most recent version of R, but not for older versions. In order to successfully install the packages provided on R-Forge, you have to switch to the most recent version of R or, alternatively, install from the package sources (.tar.gz).
Packages
| qfa | Tools for Quantitative Fitness Analysis (QFA) of Arrayed Microbial Cultures Growing on Solid Agar Surfaces | |||||||||
| Quantitative Fitness Analysis (QFA) is a complementary series of experimental and computational methods for estimating the fitness of thousands of microbial cultures in parallel. QFA is suitable for focussed, high-quality studies of the effect of genetic mutations or drug interventions on growth in model microbial organisms such as brewers yeast. Culture growth is observed by time-lapse photography of solid agar plates inoculated with cultures in rectangular arrays. Growth curves are constructed by analysing image series using Colonyzer image analysis software (http://research.ncl.ac.uk/colonyzer) which converts images to arrays of cell density estimates. This R package is for a) fitting the generalised logistic model to potentially thousands of parallel growth curves, b) using inferred parameter values to calculate fitnesses for each culture and c) comparing fitnesses between QFA experiments with different genetic backgrounds or treatments to deduce interaction strengths. This package facilitates quantifying the fitness of thousands of independent microbial strains and tracking them throughout growth curve experiments. With appropriately designed experiments, qfa can also estimate genetic interaction strengths and produce epistasis plots. | ||||||||||
| Version: 0.0-45 | Last change: 2020-02-21 19:34:37+01 | Rev.: 701 | ||||||||||
Download:
 (.tar.gz) |
 (.zip) |
Build status: Current | Stable Release: Get qfa 2.1 from CRAN | ||||||||||
R install command:
install.packages("qfa", repos="http://R-Forge.R-project.org") | ||||||||||
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| qfaBayes | Tools for modelling the growth dynamics of arrays of large numbers of colonies and performing quantitative fitness analysis (QFA). | |||||||||
| A set of tools and workflows for modelling the growth dynamics of colonies arrayed on plates, as well as performing quantitative fitness analysis (QFA) on distinct (usually genetically) types of colonies. Frequent colony growth observations are required in a specific R data.frame format. qfa can use image logs generated by Colonyzer (http://research.ncl.ac.uk/colonyzer/). You can pre-process these data with our Robot Object Database (ROD: http://sourceforge.net/projects/robotobjectdb/). The model is fit either using maximum likelihood (fast), or using a hierarchical Bayesian model for all of the colonies in an experimental unit (CPU intensive). The Bayesian fit is performed using Gibbs Sampling, implemented in C. With appropriately designed experiments, qfa can also estimate genetic interaction strengths and produce epistasis plots. | ||||||||||
| Version: 0.0-1 | Last change: 2016-01-06 17:09:07+01 | Rev.: 675 | ||||||||||
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Download:
(.tar.gz) |
(.zip) |
Build status: Current | ||||||||||
R install command:
install.packages("qfaBayes", repos="http://R-Forge.R-project.org") | ||||||||||
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Build status codes
0 - Current: the package is available for download. The corresponding package passed checks on the Linux and Windows platform without ERRORs.
1 - Scheduled for build: the package has been recognized by the build system and provided in the staging area.
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