Cedric Landerer [aut, cre],
Gabriel Hanas [ctb],
Jeremy Rogers [ctb],
Alex Cope [ctb]
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addition 'AnaCoDa' contains three currently unpublished models.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.

c(person("Cedric", "Landerer", role = c("aut", "cre"), email
= "cedric.landerer@gmail.com"), person("Gabriel", "Hanas", role
= "ctb"), person("Jeremy", "Rogers", role = "ctb"),
person("Alex", "Cope", role="ctb"), person("Denizhan", "Pak", role="ctb"))
knitr, Hmisc, VGAM, coda, testthat, lmodel2
Cedric Landerer [aut, cre],
Gabriel Hanas [ctb],
Jeremy Rogers [ctb],
Alex Cope [ctb],
Denizhan Pak [ctb]

c(person("Cedric", "Landerer", role = c("aut", "cre"), email  = "cedric.landerer@gmail.com"),
person("Gabriel", "Hanas", role = "ctb"),
person("Jeremy", "Rogers", role = "ctb"),
person("Alex", "Cope", role = "ctb"),
person("Denizhan", "Pak", role = "ctb"))

R (>= 3.3.0), Rcpp (>= 0.11.3), VGAM, methods, mvtnorm
knitr, Hmisc, coda, testthat, lmodel2, markdown

Targeted Differential and Global Enrichment Analysis of
Taxonomic Rank by Shared Asvs
person('Pierre-Louis', 'Stenger', role = c('cre','aut'), email = 'Pierrelouis.stenger@gmail.com')
ggrepel, pheatmap, lookup, plyr, data.table, rafalib,
RColorBrewer, methods, graphics

Functions for analysis of fMRI datasets stored in the ANALYZE format.
Functions for I/O, visualisation and analysis of functional Magnetic Resonance Imaging (fMRI) datasets stored in the ANALYZE format.