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 In addition 'AnaCoDa' contains three currently unpublished models.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.

Version:	0.1.4.4
Depends:	R (≥ 3.3.0), Rcpp (≥ 0.11.3), VGAM, methods, mvtnorm
LinkingTo:	Rcpp
Suggests:	knitr, Hmisc, coda, testthat, lmodel2, markdown
Published:	2020-09-15
DOI:	10.32614/CRAN.package.AnaCoDa
Author:	Authors@R
Maintainer:	Cedric Landerer <cedric.landerer at gmail.com>
License:	GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
URL:	https://github.com/clandere/AnaCoDa
NeedsCompilation:	yes
In views:	Bayesian, Omics
CRAN checks:	AnaCoDa results

Documentation:

Reference manual:	AnaCoDa.pdf
Vignettes:	Analyzing Codon Data

Downloads:

Package source:	AnaCoDa_0.1.4.4.tar.gz
Windows binaries:	r-devel: AnaCoDa_0.1.4.4.zip, r-release: AnaCoDa_0.1.4.4.zip, r-oldrel: AnaCoDa_0.1.4.4.zip
macOS binaries:	r-release (arm64): AnaCoDa_0.1.4.4.tgz, r-oldrel (arm64): AnaCoDa_0.1.4.4.tgz, r-release (x86_64): AnaCoDa_0.1.4.4.tgz, r-oldrel (x86_64): AnaCoDa_0.1.4.4.tgz
Old sources:	AnaCoDa archive

Linking:

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