Tools & Data


 

XWAS (chromosome X-Wide Analysis toolSet)

Click to visit the XWAS project's web page

Here you will find the manual, download links, references, and related information.

Gao FChang DBiddanda A, et al. "XWAS: a toolset for genetic data analysis and association studies of the X chromosome." Journal of Heredity. 2015;106(5):6.


 

EGGS (Efficient computation of Generalized-Growth  demographic models' summary Statistics)

Click to visit the EGGS project's webpage

Here you will find the manual, download links, references, and related information. 


 

Disease PCA

Click to download permutation script

Chang D, Keinan A. Principal component analysis characterizes shared pathogenetics from genome-wide association studies. PLoS computational biology.  10(9):e1003820 (2014)

 


 

 

Neutral Regions Explorer

 

  

       

          Click above to access Neutral Regions Explorer

L. Arbiza, E. Zhong, and A. Keinan. NRE: A tool for exploring neutral loci in the human genomeBMC Bioinformatics, 13, 301 (2012).

 


 

MSA (Multi-Perturbation Shapley Value Analysis)

Download MSA

A. Keinan, B. Sandbank, C. C. Hilgetag, I. Meilijson, and E. Ruppin. Fair attribution of functional contribution in artificial and biological networks. Neural Computation, 16(9), 1887-1915 (2004). 

A. Kaufman*, A. Keinan*, I. Meilijson, M. Kupiec and E. Ruppin (*equal contribution). Quantitative analysis of genetic and neuronal multi-perturbation experiments. PLoS Computational Biology, 1(6), 500-506 (2005). 

A. Keinan, B. Sandbank, C. C. Hilgetag, I. Meilijson, and E. Ruppin. Axiomatic scalable neurocontroller analysis via the Shapley value. Artificial Life, 12(3), 333-352 (2006). 

 



Datasets



 

 

E. Gazave, L. Ma, D. Chang, A. Coventry, F. Gao, D. Muzny, E. Boerwinkle, R.A. Gibbs, C.F. Sing, A.G. Clark, A. Keinan. Neutral genomic regions refine models of recent rapid human population growth.  Proceedings of the National Academy of Sciences. Early Edition Online.  Click here to download neutral regions dataset (6.3 MB).

A. Keinan, J.C. Mullikin, N. Patterson, and D. Reich. Accelerated genetic drift on chromosome X during the human dispersal out of Africa. Nature Genetics, 41(1), 66-70 (2009). Click here for dataset.