Yasui Biostatistics Research Team   

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Yutaka Yasui

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Software/Programs



Software/Programs

SNP-SNP Interactions (Dinu et al., 2012)

SAM-GS (Dinu et al., 2007)

SAM-GSR

PBEE (Martinez et al., 2007)

 

SNP-SNP Interactions Discovered by Logic Regression

• Paper:

Irina Dinu, Surakameth Mahasirimongkol, Qi Liu, Hideki Yanai, Noha Sharaf Eldin, Erin Kreiter, Xuan Wu, Shahab Jabbari, Katsushi Tokunaga, and Yutaka Yasui, "SNP-SNP Interactions Discovered by Logic Regression Explain Crohn's Disease Genetics"   PLoS ONE 7(10): e43035. doi:10.1371/journal.pone.0043035.

• Software:

To obtain the code and example datasetes, please download from here 



SAM-GS: Significant Analysis of Microarrays for Gene Sets

Gene Set Analysis Software

• Paper:

Irina Dinu, John D. Potter, Thomas Mueller, Qi Liu, Adeniyi J. Adewale, Gian S. Jhangri, Gunilla Einecke, Konrad S. Famulski, Philip Halloran, and Yutaka Yasui, "Improving GSEA for Analysis of Biologic Pathways for Differential Gene Expression across a Binary Phenotype"   (January 2007). COBRA Preprint Series. Article 16.

Dinu I, Potter JD, Mueller T, Liu Q, Adewale AJ, Jhangri GS, Einecke G, Famulski KS, Halloran P, and Yasui Y. "Improving Gene Set Analysis of Microarray Data by SAM-GS", BMC Bioinformatics 2007, 8:242

Liu Q, Dinu I, Adewale AJ, Potter JD, and Yasui Y. "Comparative Evaluation of Gene-set Analysis Methods", BMC Bioinformatics 2007, 8:431

• Software:

To obtain the free Excel Add-In software (last modified on September 5, 2012), please download EdmontonMethods.rar and the Documentation.

SAM-GS first version was made available on May 28, 2007.

R is downloadable from http://cran.r-project.org/.

R code of SAM-GS  (programmed by Irina Dinu, modified and improved by Dr. Aurelien de Reynies at Ligue Nationale Contre le Cancer, Paris. Dr. Aurelien de Reynies kindly revised the code and we reposted on April 4, 2011).

Python version of SAM-GS (developed by Dr. Simone Leo at the Advanced Computing and Communications Program of CRS4, Italy).

R code of Linear Combination Test for Hierarchical Gene Set Analysis.  

• Example datasets:

Gene-expression dataset:       p53.csv     

Gene-set-definition dataset:  c2.csv     c2part1.csv    c2part2.csv    c2.v2.symbols.gmt




SAM-GSR: Significant Analysis of Microarrays for Gene Set Reduction

• Code

R code of SAM-GSR. (Please note this is not the R code of SAM-GS. Please see above for the R code of SAM-GS)




PBEE: Population Based Estimating Equation

Integrated Estimating Equations of Individual and Aggregated Health Data

• Paper:

Jose Miguel Martinez, Joan Benach, Josep Ginebra, Fernando G. Benavides, and Yutaka Yasui (2007) "An Integrated Analysis of Individual and Aggregated Health Data Using Estimating Equations", The International Journal of Biostatistics: Vol. 3: Iss. 1, Article 10.

• Three R programs used for the simulation work:

ECC.txt    NCC.txt    SCC.txt