
PenPC
A twostep approach to estimate the skeleton of Directed Acyclic Graphs (DAGs). The first step is to estimate a partial correlation graph using penalized regression and the second step is to convert the partial correlation graph to DAG sekelton using a modified PC algorithm.

asSeq ( vignettes )
A set of tools for the study of allelespecific RNAseq data.

BPrimm
Bayesian and Penalized regression in multiple loci mapping. It includes a set of tools for simultaneously multiple loci mapping, and two novel methods named the Bayesian adaptive Lasso and the Iterative Adaptive Lasso

genoCN
Simultaneously dissect copy number states and genotypes using the
data from high density SNP arrays

isoform ( vignettes )
A set of tools for RNA isoform study using RNAseq data.

mixer
A mixture model approach to analyze ChIPchip or ChIPseq data, also with some utility functions to process DNA sequence data.

permuteP
exact permutation pvalue calculation for casecontrol study of
collapsoing a group of rare SNPs, and approximate permutation pvalue
calculation for QTL mapping in experimental cross

eMap (v1.2 Feb 2nd,
2010) ( vignettes )
eQTL computation, visiualization, eQTL module, integrated studies of complex trait, gene epression and genetic markers, etc.

censorSIR
Tools for applying Slice Inverse Regression in censored data.

ss.hmm
Segmental semiMarkov model.
