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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.
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asSeq ( vignettes )
A set of tools for the study of allele-specific RNA-seq data.
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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
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genoCN
Simultaneously dissect copy number states and genotypes using the
data from high density SNP arrays
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isoform ( vignettes )
A set of tools for RNA isoform study using RNA-seq data.
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mixer
A mixture model approach to analyze ChIP-chip or ChIP-seq data, also with some utility functions to process DNA sequence data.
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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
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eMap (v1.2 Feb 2nd,
2010) ( vignettes )
eQTL computation, visiualization, eQTL module, integrated studies of complex trait, gene epression and genetic markers, etc.
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censorSIR
Tools for applying Slice Inverse Regression in censored data.
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ss.hmm
Segmental semi-Markov model.
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