R Packages
  • PenPC
    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.

  • 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 RNA-seq data.

  • mixer
    A mixture model approach to analyze ChIP-chip or ChIP-seq data, also with some utility functions to process DNA sequence data.

  • permuteP
    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.

  • censorSIR
    Tools for applying Slice Inverse Regression in censored data.

  • ss.hmm
    Segmental semi-Markov model.

Others (programming for fun)
  • simulated annealing
    Use simulated annealing method to solve the sudoku puzzle.

  • option
    Calculate profit of option investment using combination of bear spread and bull spread.