Software

(24) R codes for Bivariate Stochastic Functional Linear Models for Gene-based Association Analysis of Quantitative Traits in Longitudinal Studies

• • Zip file: R codes 

• Zip file: Data 

• PDF documentation.

(23) R codes for Deconvolution Analysis of Spatial Transcriptomics by Multiplicative-Additive Poisson-gamma Models

• • Zip file: R codes 

• Zip file: Data 

• PDF documentation.

(22) R codes for Gene-level Association Analysis of Bi-variate Ordinal Traits with Functional Regressions

• • Zip file: R codes 

• Zip file: Data 

• PDF documentation.

(21) R codes for Stochastic Generalized Functional Linear Models for Gene-based Association Analysis of Binary Traits in Longitudinal Studies 

• • Zip file: R codes 

• Zip file: Data 

• PDF documentation.

(20) R codes for Deconvolution Analysis of Cell Type Expression from Bulk Tissues by Integrating with Single-cell Expression Reference21

• • Zip file: R codes 

• PDF documentation

(19) R codes for Gene-level Association Analysis of Ordinal Traits with Functional Ordinal Logistic Regressions 

• • Zip file: R codes 

• Zip file: Data 

• PDF documentation.

(18) R codes for Gene-based analysis of bi-variate survival traits via functional regressions

• • Zip file: R codes 

• Zip file: Data 

• PDF documentation.

(17) R codes for Stochastic Functional Linear Models for Gene-based Association Analysis of Quantitative Traits in Longitudinal Studies

• • Zip file: R codes 

• Zip file: Data 

• PDF documentation.

(16) R codes for Gene-based Association Analysis of Survival Traits via Functional Regression-based Mixed Effect Cox Models for Related Samples

• Zip file: R codes 

• PDF documentation.

(15) R package for Gene-Based Association Testing pf Dichotomous Traits with Generalized Linear Mixed Models for Family Data

• •  R Package: PedGFLMM

(14) R codes for Linear Mixed Models for Association Analysis of Quantitative Traits with Next-generation Sequencing Data

• Zip file: R codes 

• Zip file: Data 

• PDF documentation.

(13) R codes for Gene Level Meta-analysis of Quantitative Pleiotropic Traits with Multivariate Functional Linear Models

• Zip file: R codes 

• PDF documentation.

(12) R codes for Cox FR LRT: a Gene-based Association Method for Censored Traits Via Functional Regressions, R. Fan and Q. Yan

• Zip file: R codes

• PDF documentation.

(11) R Codes for Gene Level Meta-analysis of Quantitative Traits by Functional Linear Models, R. Fan, 2015.

• Zip file: R codes

• PDF documentation.

(10) R codes for Gene Level Meta-analysis of Dichotomous Traits by Generalized Functional Linear Models, R. Fan

• Zip file: R codes

• PDF documentation.

(9) Datasets to run functional regression models in (6), (7), and (8) below

• • Zip file: Datasets to run functional regression models (ZIP - 8.29 KB)

• cov1.csv

• gene_annotation.csv

• gene_map.csv

  • geno1.csv 

• y1.csv

• y2.csv

• yc.csv

(8) Pleiotropy Analysis of Quantitative Traits at Gene Level by Multivariate Functional Linear Models, R. Fan and Y. Wang

• Zip file: R codes

• PDF Documentation

(7) Generalized Functional Linear Models for Gene-based Case-Control Association Studies, R. Fan and Y. Wang

• Zip file: R codes

• PDF Documentation

(6) Functional Linear Models for Association Analysis of Quantitative Traits, by R. Fan and Y. Wang

• Zip file: R codes

• PDF Documentation

(5) Association analysis of complex diseases using triads, parent-child dyads and singleton monads, by R. Fan and A. Lee

• • PDF Documentation 

Joint_Association_Analysis_web

• • Zip file: Joint_Association_Analysis_web (ZIP - 8.7 KB)

• Additive

• Dominant

• Multiplicative

• Recessive

• Unrestricted (General)

• Monad

• Dyad

• Triad

• Example file

Count_Triad_Dyad_Monad

• • Zip file: Count_Triad_Dyad_Monad (ZIP - 30 KB)

• R_out

• count_triad_dyad_monad.R

• sas_out

• count_triad_dyad_monad.sas

• simped.csv

• simped_READ_ME

(4) Longitudinal association analysis of quantitative traits, R. Fan, 2015

• Zip file

• PDF Documentation

(3) R codes for Entropy-based Information Gain Approaches to Detect Gene-Gene and Gene-Environment Interactions/Correlations of Complex Diseases, R. Fan, 2015

• • Zip file: R codes 

(2) Hotelling T^2 Tests, by R. Fan and M. Knapp

(a) Hotelling T^2 Tests Based on Population Case Control Data

• • Documentation: Hotelling T^2 Tests Based on Population Case Control Data (PDF - 58 KB)

  • SAS Macro

  • Example file

• Example data

(b) Hotelling T^2 Tests Based on Nuclear Trio Family Data

• • Documentation: Hotelling T^2 Tests Based on Nuclear Trio Family Data (PDF - 66 KB)

• SAS Macro

• Example file

• Example data

(c) Hotelling T^2 Tests Based on Sib-ship Data

• • Documentation: Hotelling T^2 Tests Based on Sib-ship Data (PDF - 64 KB)

• SAS Macro

• Example file

• Example data

(1) Software to Detect Positive Selection in the Human Genome, by R. Fan and M. Zhong

(a) Extended Homozygosity Score Test (EHST)

• • PDF Documentation 

  • C++ codes and Makefile

  • EGHH.cc

  • EGHH.h

  • Makefile

  • Repeater1_EGHH

An example of HapMap II data:

• • YRI chromosome 2 legend data (TXT - 5.7 MB)

  • YRI chromosome 2 haplotype phase data (TXT - 58 MB)

(b) A Cross-population Extended Haplotype-based Homozygosity Score Test (xp-EHHST)

• • Documentation: A Cross-population Extended Haplotype-based Homozygosity Score Test (PDF - 39 KB)

  • C++ codes and Makefile

  • xpEHHST.cc

  • xpEHHST.h

  • Makefile

An example of HapMap II data:

• • CEU chromosome 2 legend data (TXT - 200 KB)

  • CEU chromosome 2 haplotype phase data (TXT - 51 MB)

  • CHB+JPT chromosome 2 legend data (TXT - 4.7 MB)

  • CHB+JPT chromosome 2 haplotype phase data (TXT - 71 MB)

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