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 brewer's 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.

AuthorConor Lawless <conor.lawless@ncl.ac.uk>, with contributions from Alexander Young <alextisyoung@gmail.com> and Darren Wilkinson <d.j.wilkinson@ncl.ac.uk>
Date of publication2016-12-01 17:32:23
MaintainerConor Lawless <conor.lawless@ncl.ac.uk>
LicenseArtistic-2.0
Version0.0-43
http://qfa.r-forge.r-project.org/

View on R-Forge

Man pages

checkTarg: checkTarg

colonyzer.read: Reads raw cell density timecourse data from Colonyzer output...

correlationReport: Correlation Report

datafit: Fitting generalised logistic model to growth data by least...

dtl: Culture Doubling Time for Generalised Logistic Function (as a...

fitnessReport: Fitness Report

getDeadLocations: Find dead cultures in SGA plates (1536 format), and report...

getMissingGenotypes: getMissingGenotypes

getMissingSGA: getMissingSGA

getNeighbours: getNeighbours

Glogist: Generalised Logistic growth curve model

growthcurve: Wrapper function for generating QFA generalised logistic...

iRVisDemo: Interactive fitness plots from Addinal et al. 2011 PLoS...

loapproxfun: Model free growth curve approximation

logist: Logistic growth curve model

makeBoundsQFA: Generate generalised logistic parameter bounds for QFA

makeFitness: Generate QFA fitnesses

mdp: Maximum Doubling Potential (MDP) for Generalised Logistic...

mdr: Maximum Doubling Rate (MDR) for Generalised Logistic Function

mdrmdp: Fitness value for Generalised Logistic Function

normalisePlates: Normalising culture fitness by plate

numericalfitness: Numerical fitness estimates from timecourse data

numerical_r: Generates numerical fitnesses from experimental growth curve...

pgis: Calculate strength and significance of genetic interaction.

plateBoxplots: Plate Boxplots

qfa.epi: Finds genetic interaction strengths and p-values

qfa.epiplot: Makes an epistasis plot from the full results of qfa.epi

qfa.fit: Growth curve modelling

qfa-Internal: Internal qfa Functions

qfa.plot: Plots fitted model and data for all the colonies in results...

readMer: readMer

readSGD: readSGD

report.epi: Normalising culture fitness by plate

rod.read: Reading of ROD raw timecourse data. Deprecated.

rod.write: Writes a synthetic ROD-like output file to hard-drive....

showDemo: Show Demo

visTool: Making the visualisation tool

Files in this package

qfa/DESCRIPTION
qfa/NAMESPACE
qfa/R
qfa/R/Exponential.R qfa/R/Profiling.R qfa/R/Visualisation.R qfa/R/colonyRead.R qfa/R/compareFitnesses.R qfa/R/filteringGenes.R qfa/R/qfa.R qfa/R/reports.R qfa/R/rodRead.R qfa/R/stripSGA.R qfa/R/visualiseCurves.R
qfa/build
qfa/build/vignette.rds
qfa/demo
qfa/demo/00Index
qfa/demo/fittingGrowthCurves.R
qfa/demo/telomereCap.R
qfa/inst
qfa/inst/doc
qfa/inst/doc/iRVis.Rmd
qfa/inst/doc/iRVis.html
qfa/inst/doc/qfa.Snw
qfa/inst/doc/qfa.pdf
qfa/inst/extdata
qfa/inst/extdata/DAL_QFA0139_Yku70_23_SDM_rhk_CTGN_vs_QFA0141_ura3_20_SDM_rhk_CTGN_MDRMDP_GIS.txt
qfa/inst/extdata/DAL_QFA0139_Yku70_30_SDM_rhk_CTGN_vs_QFA0141_ura3_27_SDM_rhk_CTGN_MDRMDP_GIS.txt
qfa/inst/extdata/DAL_QFA0139_Yku70_37_5_SDM_rhk_CTGN_vs_QFA0141_ura3_37_SDM_rhk_CTGN_MDRMDP_GIS.txt
qfa/inst/extdata/DAL_QFA0139_Yku70_37_SDM_rhk_CTGN_vs_QFA0141_ura3_37_SDM_rhk_CTGN_MDRMDP_GIS.txt
qfa/inst/extdata/DAL_QFA0140_cdc13-1_20_SDM_rhlk_CTGH_vs_QFA0141_ura3_20_SDM_rhk_CTGN_MDRMDP_GIS.txt
qfa/inst/extdata/DAL_QFA0140_cdc13-1_27_SDM_rhlk_CTGH_vs_QFA0141_ura3_27_SDM_rhk_CTGN_MDRMDP_GIS.txt
qfa/inst/extdata/DAL_QFA0140_cdc13-1_36_SDM_rhlk_CTGH_vs_QFA0141_ura3_37_SDM_rhk_CTGN_MDRMDP_GIS.txt
qfa/inst/extdata/DAL_QFA0141_ura3_27_SDM_rhk_CTGN_vs_QFA0141_ura3_20_SDM_rhk_CTGN_MDRMDP_GIS.txt
qfa/inst/extdata/DAL_QFA0141_ura3_37_SDM_rhk_CTGN_vs_QFA0141_ura3_20_SDM_rhk_CTGN_MDRMDP_GIS.txt
qfa/inst/extdata/FunctionalComplexes.txt
qfa/inst/extdata/GOAnnotation.txt
qfa/inst/extdata/GenerateDemoFiles.R
qfa/inst/extdata/LibraryDescription.txt
qfa/inst/extdata/ORF2GENE.txt
qfa/inst/extdata/SGD_features.tab
qfa/inst/extdata/URA3Control.dat
qfa/inst/extdata/URA3ExptDescription.txt
qfa/inst/extdata/cdc13-1ExptDescription.txt
qfa/inst/extdata/cdc13-1Query.dat
qfa/inst/extdata/pombeGOAnnotation.dat
qfa/inst/extdata/pombeGOAnnotation.txt
qfa/man
qfa/man/Glogist.Rd qfa/man/checkTarg.Rd qfa/man/colonyzer.read.Rd qfa/man/correlationReport.Rd qfa/man/datafit.Rd qfa/man/dtl.Rd qfa/man/fitnessReport.Rd qfa/man/getDeadLocations.Rd qfa/man/getMissingGenotypes.Rd qfa/man/getMissingSGA.Rd qfa/man/getNeighbours.Rd qfa/man/growthcurve.Rd qfa/man/iRVisDemo.Rd qfa/man/loapproxfun.Rd qfa/man/logist.Rd qfa/man/makeBoundsQFA.Rd qfa/man/makeFitness.Rd qfa/man/mdp.Rd qfa/man/mdr.Rd qfa/man/mdrmdp.Rd qfa/man/normalisePlates.Rd qfa/man/numerical_r.Rd qfa/man/numericalfitness.Rd qfa/man/pgis.Rd qfa/man/plateBoxplots.Rd qfa/man/qfa-Internal.Rd qfa/man/qfa.epi.Rd qfa/man/qfa.epiplot.Rd qfa/man/qfa.fit.Rd qfa/man/qfa.plot.Rd qfa/man/readMer.Rd qfa/man/readSGD.Rd qfa/man/report.epi.Rd qfa/man/rod.read.Rd qfa/man/rod.write.Rd qfa/man/showDemo.Rd qfa/man/visTool.Rd
qfa/vignettes
qfa/vignettes/QFAVisualisation0001.png
qfa/vignettes/QFAVisualisation0002.png
qfa/vignettes/QFAVisualisation0003.png
qfa/vignettes/RatioPlot0001.png
qfa/vignettes/RatioPlot0002.png
qfa/vignettes/RatioPlot0002a.png
qfa/vignettes/RatioPlot0003.png
qfa/vignettes/RatioPlot0004.png
qfa/vignettes/RatioPlot0005.png
qfa/vignettes/RatioPlot0006.png
qfa/vignettes/RatioPlot0007.png
qfa/vignettes/RatioPlot0008.png
qfa/vignettes/iRVis.Rmd
qfa/vignettes/qfa.Snw

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