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 In addition 'AnaCoDa' contains three currently unpublished models.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: 0.1.2
Depends: R (≥ 3.3.0), Rcpp (≥ 0.11.3), methods
LinkingTo: Rcpp
Suggests: knitr, Hmisc, VGAM, coda, testthat, lmodel2
Published: 2018-09-14
Author: Cedric Landerer [aut, cre], Gabriel Hanas [ctb], Jeremy Rogers [ctb], Alex Cope [ctb], Denizhan Pak [ctb]
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
Materials: README NEWS
CRAN checks: AnaCoDa results

Downloads:

Reference manual: AnaCoDa.pdf
Vignettes: Analyzing Codon Data
Package source: AnaCoDa_0.1.2.tar.gz
Windows binaries: r-devel: AnaCoDa_0.1.2.zip, r-release: AnaCoDa_0.1.2.zip, r-oldrel: AnaCoDa_0.1.2.zip
OS X binaries: r-release: AnaCoDa_0.1.1.tgz, r-oldrel: AnaCoDa_0.1.2.tgz
Old sources: AnaCoDa archive

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