Free Download of Our Software Packages

 

 

Genomic and Protein Sequence Analysis

Genomic, Expression and Pathway Analysis

Genetic Linkage Analysis

Gene Array Data Analysis

Statistical Analysis of Human Nondisjunction Data

Population Genetics

Modifier Gene Analysis

 

 

Genomic and Protein Sequence Analysis

Workflow for data pre-processing of multiple reaction monitoring (MRM) experiments. It includes data quality assessment and normalization.

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An M package for Clustering 16S rRNA sequences into OTUs. The download link contain the package and some benchmark data sets.

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iPAC (Identification of Protein Amino acid mutation Clustering) finds mutation clusters on the amino acid level while taking into account the protein structure. 

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A pipeline to adjust the biases and errors of sequencing data to gain more accurate allele frequency estimation.

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An R package for detecting and correcting biases in RNA-Sequencing data. The download link contains the package, the manual and a "vignette" for quick start.

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A bioconductor R package for identifying mutational clusters of amino acids in a protein while utilizing the protein tertiary structure via a graph theoretical model.

Link to the software

An R package providing exploratory graphics and qualify assessment for MRM data generated from Multiquant (ABSciex) and SWATH datasets.

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An R code for Bayesian modeling of paired RNA-seq experiment.

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Genomic, Expression and Pathway Analysis

This is an R package implementing a post-GWAS prioritization algorithm, which incorporates the rewiring information of co-expression network to prioritize GWAS signals.

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MCMG is designed to infer the gene-microRNA interaction pairs from joint analysis of multiple cancers.

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A LOw-Rank representation and Sparse regression for eQTL mapping. This algorithm accounts for confounding factors such as unobserved covariates, experimental artifacts, and unknown environmental perturbations.

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An R package implementing a phylogenetic tree based method to model the on/off rates of transcription factor binding (TFB) events, and uses the EM algorithm to estimate model parameters.

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 An R package implementing a bayesian sparse factor model for the joint analysis of paired datasets, the gene expression and drug sensitivity profiles, measured across the same panel of samples, e.g. cell lines.

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An R package implementing a Bayesian sparse factor model for the inference of pathways responsive to drug treatment.

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 An improved SNP calling algorithm for Illumina BeadArry Data.

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Genetic Linkage Analysis

Gene Array Data Analysis

Statistical Analysis of human nondisjunction Data

Population Genetics

 

Modifier Gene Analysis


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