This package is considered a duplicate. The official version of this package is found at:https://clandere.r-universe.dev/AnaCoDa

Package: AnaCoDa 0.1.4.4

Cedric Landerer

AnaCoDa: Analysis of Codon Data under Stationarity using a Bayesian Framework

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) <doi:10.1093/gbe/evv087>), and ROC with phi (Wallace & Drummond (2013) <doi:10.1093/molbev/mst051>). In addition 'AnaCoDa' contains three currently unpublished models.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.

Authors:Authors@R

AnaCoDa_0.1.4.4.tar.gz
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AnaCoDa_0.1.4.4.tgz(r-4.4-emscripten)AnaCoDa_0.1.4.4.tgz(r-4.3-emscripten)
AnaCoDa.pdf |AnaCoDa.html✨
AnaCoDa/json (API)

# Install 'AnaCoDa' in R:

install.packages('AnaCoDa', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/clandere/anacoda/issues

Uses libs:

c++– GNU Standard C++ Library v3
openmp– GCC OpenMP (GOMP) support library

cpp openmp

3.00 score 100 scripts 331 downloads 1 mentions 35 exports 3 dependencies

Last updated 4 years agofrom:fd37528885. Checks:OK: 1 NOTE: 1. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Dec 27 2024
R-4.5-linux-x86_64	NOTE	Dec 27 2024

Exports:AAToCodon acfCSP acfMCMC addObservedSynthesisRateSet aminoAcids calculateMarginalLogLikelihood calculateSCUO codons codonToAA convergence.test findOptimalCodon geomMean getCAI getCAIweights getCodonCounts getCodonCountsForAA getCSPEstimates getExpressionEstimates getMixtureAssignmentEstimate getNames getNc getNcAA getObservedSynthesisRateSet getSelectionCoefficients getTrace initializeGenomeObject initializeMCMCObject initializeModelObject initializeParameterObject loadMCMCObject loadParameterObject runMCMC setRestartSettings writeMCMCObject writeParameterObject

Dependencies:mvtnorm Rcpp VGAM

AnaCoDa: Analyzing Codon Data

Cedric Landerer & Alexander L. Cope

Rendered fromanacoda.Rmdusingknitr::rmarkdownon Dec 27 2024.

Last update: 2020-09-15
Started: 2018-09-14

Help page	Topics
Amino Acid to codon set	AAToCodon
Plots ACF for codon specific parameter traces	acfCSP
Autocorrelation function for the likelihood or posterior trace	acfMCMC
Add gene observed synthesis rates	addObservedSynthesisRateSet
Amino acids	aminoAcids
Calculates the marginal log-likelihood for a set of parameters	calculateMarginalLogLikelihood
calculates the synonymous codon usage order (SCUO)	calculateSCUO
Codons	codons
translates codon to amino acid	codonToAA
Convergence Test	convergence.test
Find and return list of optimal codons	findOptimalCodon
fixDEta	fixDEta
fixDM	fixDM
fixSphi	fixSphi
Take the geometric mean of a vector	geomMean
getAdaptiveWidth	getAdaptiveWidth
Calculate the Codon Adaptation Index	getCAI
Calculate the CAI codon weigths for a reference genome	getCAIweights
Get Codon Counts For all Amino Acids	getCodonCounts
Get Codon Counts For a specific Amino Acid	getCodonCountsForAA
getCodonSpecificPosteriorMeanForCodon	getCodonSpecificPosteriorMeanForCodon
getCodonSpecificPosteriorVarianceForCodon	getCodonSpecificPosteriorVarianceForCodon
getCodonSpecificQuantilesForCodon	getCodonSpecificQuantilesForCodon
Return Codon Specific Paramters (or write to csv) estimates as data.frame	getCSPEstimates
getEstimatedMixtureAssignmentForGene	getEstimatedMixtureAssignmentForGene
getEstimatedMixtureAssignmentProbabilitiesForGene	getEstimatedMixtureAssignmentProbabilitiesForGene
Returns the estimated phi posterior for a gene	getExpressionEstimates
getGroupList	getGroupList
getLogLikelihoodTrace	getLogLikelihoodTrace
getLogPosteriorMean	getLogPosteriorMean
getLogPosteriorTrace	getLogPosteriorTrace
Returns mixture assignment estimates for each gene	getMixtureAssignmentEstimate
Gene Names of Genome	getNames
Calculate the Effective Number of Codons	getNc
Calculate the Effective Number of Codons for each Amino Acid	getNcAA
getNoiseOffsetPosteriorMean	getNoiseOffsetPosteriorMean
getNoiseOffsetVariance	getNoiseOffsetVariance
Get gene observed synthesis rates	getObservedSynthesisRateSet
getSamples	getSamples
Calculate Selection coefficients	getSelectionCoefficients
getStdDevSynthesisRatePosteriorMean	getStdDevSynthesisRatePosteriorMean
getStdDevSynthesisRateVariance	getStdDevSynthesisRateVariance
getStepsToAdapt	getStepsToAdapt
getSynthesisRate	getSynthesisRate
getSynthesisRatePosteriorMeanForGene	getSynthesisRatePosteriorMeanForGene
getSynthesisRatePosteriorVarianceForGene	getSynthesisRatePosteriorVarianceForGene
getThinning	getThinning
extracts an object of traces from a parameter object.	getTrace
getTraceObject	getTraceObject
Initialize Covariance Matrices	initializeCovarianceMatrices
Genome Initialization	initializeGenomeObject
Initialize MCMC	initializeMCMCObject
Model Initialization	initializeModelObject
Initialize Parameter	initializeParameterObject
initializeSynthesisRateByGenome	initializeSynthesisRateByGenome
initializeSynthesisRateByList	initializeSynthesisRateByList
initializeSynthesisRateByRandom	initializeSynthesisRateByRandom
initMutationCategories	initMutationCategories
initSelectionCategories	initSelectionCategories
Length of Genome	length.Rcpp_Genome
Load MCMC Object	loadMCMCObject
Load Parameter Object	loadParameterObject
Plot Model Object	plot.Rcpp_FONSEModel
Plot Parameter	plot.Rcpp_FONSEParameter
Plot MCMC algorithm	plot.Rcpp_MCMCAlgorithm
Plot Model Object	plot.Rcpp_ROCModel
Plot Parameter	plot.Rcpp_ROCParameter
Plot Trace Object	plot.Rcpp_Trace
Plot Acceptance ratios	plotAcceptanceRatios
Plot Codon Specific Parameter	plotCodonSpecificParameters
readPhiValue	readPhiValue
Run MCMC	runMCMC
setAdaptiveWidth	setAdaptiveWidth
setGroupList	setGroupList
setRestartFileSettings	setRestartFileSettings
Set Restart Settings	setRestartSettings
setSamples	setSamples
setStepsToAdapt	setStepsToAdapt
setThinning	setThinning
simulateGenome	simulateGenome
Summary of Genome	summary.Rcpp_Genome
Write MCMC Object	writeMCMCObject
Write Parameter Object to a File	writeParameterObject

Package: AnaCoDa 0.1.4.4

AnaCoDa: Analysis of Codon Data under Stationarity using a Bayesian Framework

AnaCoDa: Analyzing Codon Data

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