A two-step 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 allele-specific RNA-seq data.
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
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 RNA-seq data.
A mixture model approach to analyze ChIP-chip or ChIP-seq data, also with some utility functions to process DNA sequence data.
exact permutation p-value calculation for case-control study of
collapsoing a group of rare SNPs, and approximate permutation p-value
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.
Tools for applying Slice Inverse Regression in censored data.
Segmental semi-Markov model.