Automagically Document and Install Packages Necessary to Run R Code (automagic)
Parse R code in a given directory for R packages and attempt to install them from CRAN or GitHub. Optionally use a dependencies file for tighter control over which package versions to install.

Nested Association Mapping Analysis (NAM)
Designed for association studies in nested association mapping (NAM) panels, also handling biparental and random panels. It includes functions for genome-wide associations mapping of multiple populations, marker quality control, solving mixed models and finding variance components through REML and Gibbs sampling.

Array CGH Data Analysis and Visualization (cghRA)
Provides functions to import data from Agilent CGH arrays and process them according to the cghRA workflow. Implements several algorithms such as WACA, STEPS and cnvScore and an interactive graphical interface.

Multilevel Index of Dissimilarity (MLID)
Tools and functions to fit a multilevel index of dissimilarity.

The q-Gaussian Distribution (qGaussian)
Density, distribution function, quantile function and random generation for the q-gaussian distribution with parameters mu and sig.