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AnaCoDa  

Analysis of Codon Data under Stationarity using a Bayesian Framework
View on CRAN: Click here


Download and install AnaCoDa package within the R console
Install from CRAN:
install.packages("AnaCoDa")

Install from Github:
library("remotes")
install_github("cran/AnaCoDa")

Install by package version:
library("remotes")
install_version("AnaCoDa", "0.1.4.4")



Attach the package and use:
library("AnaCoDa")
Maintained by
Cedric Landerer
[Scholar Profile | Author Map]
First Published: 2018-01-11
Latest Update: 2020-09-15
Description:
Is a collection of models to analyze genome scale codon data using a Bayesian framework. Provides visualization routines and checkpointing for model fittings. Currently published models to analyze gene data for selection on codon usage based on Ribosome Overhead Cost (ROC) are: ROC (Gilchrist et al. (2015) ), and ROC with phi (Wallace & Drummond (2013) ). In addition 'AnaCoDa' contains three currently unpublished models. The FONSE (First order approximation On NonSense Error) model analyzes gene data for selection on codon usage against of nonsense error rates. The PA (PAusing time) and PANSE (PAusing time + NonSense Error) models use ribosome footprinting data to analyze estimate ribosome pausing times with and without nonsense error rate from ribosome footprinting data.
How to cite:
Cedric Landerer (2018). AnaCoDa: Analysis of Codon Data under Stationarity using a Bayesian Framework. R package version 0.1.4.4, https://cran.r-project.org/web/packages/AnaCoDa. Accessed 21 Feb. 2025.
Previous versions and publish date:
0.1.0 (2018-01-11 13:01), 0.1.1 (2018-02-13 00:14), 0.1.2.1 (2018-11-27 18:30), 0.1.2.2 (2019-03-04 10:20), 0.1.2.3 (2019-03-15 18:18), 0.1.2 (2018-09-14 18:10), 0.1.3.0 (2019-05-12 00:12)
Other packages that cited AnaCoDa R package
View AnaCoDa citation profile
Other R packages that AnaCoDa depends, imports, suggests or enhances
Complete documentation for AnaCoDa
Functions, R codes and Examples using the AnaCoDa R package
Some associated functions: AAToCodon . acfCSP . acfMCMC . addObservedSynthesisRateSet . aminoAcids . calculateMarginalLogLikelihood . calculateSCUO . codonToAA . codons . convergence.test . findOptimalCodon . fixDEta . fixDM . fixSphi . geomMean . getAdaptiveWidth . getCAI . getCAIweights . getCSPEstimates . getCodonCounts . getCodonCountsForAA . getCodonSpecificPosteriorMeanForCodon . getCodonSpecificPosteriorVarianceForCodon . getCodonSpecificQuantilesForCodon . getEstimatedMixtureAssignmentForGene . getEstimatedMixtureAssignmentProbabilitiesForGene . getExpressionEstimates . getGroupList . getLogLikelihoodTrace . getLogPosteriorMean . getLogPosteriorTrace . getMixtureAssignmentEstimate . getNames . getNc . getNcAA . getNoiseOffsetPosteriorMean . getNoiseOffsetVariance . getObservedSynthesisRateSet . getSamples . getSelectionCoefficients . getStdDevSynthesisRatePosteriorMean . getStdDevSynthesisRateVariance . getStepsToAdapt . getSynthesisRate . getSynthesisRatePosteriorMeanForGene . getSynthesisRatePosteriorVarianceForGene . getThinning . getTrace . getTraceObject . initMutationCategories . initSelectionCategories . initializeCovarianceMatrices . initializeGenomeObject . initializeMCMCObject . initializeModelObject . initializeParameterObject . initializeSynthesisRateByGenome . initializeSynthesisRateByList . initializeSynthesisRateByRandom . length.Rcpp_Genome . loadMCMCObject . loadParameterObject . plot.Rcpp_FONSEModel . plot.Rcpp_FONSEParameter . plot.Rcpp_MCMCAlgorithm . plot.Rcpp_ROCModel . plot.Rcpp_ROCParameter . plot.Rcpp_Trace . plotAcceptanceRatios . plotCodonSpecificParameters . readPhiValue . runMCMC . setAdaptiveWidth . setGroupList . setRestartFileSettings . setRestartSettings . setSamples . setStepsToAdapt . setThinning . simulateGenome . summary.Rcpp_Genome . writeMCMCObject . writeParameterObject . 
Some associated R codes: RcppExports.R . colorSchemes.R . genomeObject.R . mcmcObject.R . modelObject.R . onloadPackage.R . parameterObject.R . plotMCMCAlgorithmObject.R . plotModelObject.R . plotParameterObject.R . plotTraceObject.R . traceObject.R .  Full AnaCoDa package functions and examples
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