qfaBayes: Tools for modelling the growth dynamics of arrays of large numbers of colonies and performing quantitative fitness analysis (QFA).
Version 0.0-1

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.

Getting started

Package details

AuthorJonathan Heydari <j.j.heydari@ncl.ac.uk>, with contributions from Conor Lawless <conor.lawless@ncl.ac.uk> and Darren Wilkinson <d.j.wilkinson@ncl.ac.uk>
Date of publication2016-01-06 16:09:07
MaintainerConor Lawless <conor.lawless@ncl.ac.uk>
URL http://qfa.r-forge.r-project.org/
Package repositoryView on R-Forge
Installation Install the latest version of this package by entering the following in R:
install.packages("qfaBayes", repos="http://R-Forge.R-project.org")

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qfaBayes documentation built on May 31, 2017, 1:30 a.m.