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Software Programs from Hongzhe Li's Group


<marquee>Programs</marquee>

SUMMARY
Supported by NIH grants ES009911, CA127334 and GM097505, we have developed statistical and computational methods for analysis of genetic, genomics and microbiome data. We list here the programs that implement some of our latest statistical methods, most are written in R and are available as Cran-R packages. Some datasets can also be found here. Note that these program are constantly beining updated. For questions and comments, please email Dr. Hongzhe Li, (hongzhe@upenn.edu) .

LIST OF PROGRAMS
GUniFrac, MCLIME, HighDCox, DirMulti, HeteroReg, qMSAT, LRS, MATCHCLIP, CNVtest.

Download FDE
This program .zip file includes Matlab codes and real data sets used in paper on estimating genetic relatedness of two traits based on large scale genetic association data.
Guo Z, Wang W, Cai, TT and Li H (2017 JASA).
Source code language: Mathlab.

Download Modified Rank Tests
This program .zip file includes R codes and real data sets used in paper on modified rank tests for data with excessive zeros.
Wang W, Chen EZ and Li H (2017 submitted).
Source code language: R codes.

GUniFrac
This program is available as a cran-R package (link here) that implements a generalized UniFrac distance for analysis of microbiome data
Chen J and Li H (2012).
Source code language: R.

MCLIME
This program is available as a cran-R package (link here) that implements simultaneous estimation of the regression coefficients and precision matrix.
Xie J, Cai T and Li H (2012).
Source code language: R/Splus.

HighDCox
The following is a list of R programs for linking the microarray gene expression data to censroed survival data. Dataexample.R includes examples of using these functions using simulated data sets. Further details of the functions can be found in this documentmetaion (pdf file) of the programs.

References:
  1. Li H , Gui J(2004): Partial Cox Regression Analysis for High-Dimensional Microarray Gene Expression Data. Bioinformatics , 20(suppl 1), i208-i215. (pdf file)
  2. Gui J, Li H (2005): Penalized Cox Regression Analysis in the High-Dimensional and Low-sample Size Settings, with Applications to Microarray Gene Expression Data. Bioinformatics , 21: 3001-3008.
Programs:
  1. Partial Cox regression method ( Li and Gui, 2004 ).
    • Download program: PCRCox
      A collection of R/Splus programs.
    • Source code language: R/Splus.
  2. Threshold gradient descent methods for fitting the Cox model ( Gui and Li, 2005 ).
    • Download program: TGDCox
      A collection of R/Splus programs.
    • Source code language: R/Splus.
DirMulti
Variable selection for Dirichlet-Multinomial regression for identifying covariates that are associated with microbiomes. Download Porgram Here
Chen J, Li H (2012): Annals of Applied Statistics (revision).
Source codes: R/Splus.

LRS
Likelihoo ratio selector for identifying the copy number variants (CNVs) for the SNP Chip LogR ratio data.
Jeng J, Cai TT and Li H (2010): Optimal sparse segment identification with application in copy number variation analysis. Journal of American Statistical Association, 105 (491): 1156-1166. Download Porgram Here
Source codes: R/Splus.

HeteroReg
Variable selction for high dimesional Heteroscedastic Regression.
Daye J, Chen J and Li H (2012): High-dimensional heteroscedastic regression with an application to eQTL data analysis Biometrics, 68: 316-326. Download Porgram Here
Source codes: Fortran and R/Splus.


qMSAT
A Quality-based Multivariate Score Association Test.
Z. John Daye, Hongzhe Li, and Zhi Wei (2012): A Powerful Test for Multiple Rare Variants Association Studies that Incorporate Sequencing Qualities. Nucleic Acids Research, in press
See link to the pogram here qMAST

MATCHCLIP
Program for identifying the breakpoints and CNVs based on the next generation sequence data using CIGAR strings.
Wu Y, Tian L, Pirastu M, Stambolian D, Li H(2013): MATCHCLIP: Locate precise break points for copy number variation using CIGAR strings.
See link to the pogram here MATCHCLIP

CNVtest
R Program for testing CNV associtiob based on SNP array log-ratio data for both case-control and quantative traits.
Jeng J, Wu Q and Li H (2015): A Statistical Method for Identifying Trait-Associated Copy Number Variants. Download Porgram Here
Source codes: R/Splus.

Page Updated: Jan 2012
Page URL: http://statgene.med.upenn.edu/softprog.html
Page Author: Hongzhe Li.