Software

 

MT-eQTL: Empirical Bayes method for multi-tissue expression quantitative trait loci (eQTL) analysis

An empirical Bayes approach for multiple tissue eQTL analysis, G. Li, A.A. Shabalin, I. Rusyn, F.A. Wright, A.B. Nobel, arXiv:1311.2948, 2016.

Software Website

 

DCM: Method for finding sets of differentially correlated variables in case-control data

A testing-based approach to the discovery of differentially correlated variable sets, K. Bodwin, K. Zhang, and A.B. Nobel, https://arxiv.org/abs/1509.08124v2.

Software Website

 

ESSC: Community detection procedure for unweighted networks

A testing based extraction algorithm for identifying significant communities in networks, J.D. Wilson, S. Wang, P.J. Mucha, S. Bhamidi, and A.B. Nobel, Annals of Applied Statistics vol.8, No. 3, 1853-1891, 2015.

Software Website

 

SigClust: Permutation based method for assessing the significance of clustering results

Statistical significance of clustering for high-dimension, low-sample size data, Y. Liu, D.N. Hayes, A.B. Nobel and J.S. Marron, Journal of the American Statistical Association, vol.103 pp.1281-1293, 2008.

Statistical significance of clustering using soft thresholding,  H. Huang, Y. Liu, M. Yuan, and J. S. Marron, arXiv:1305.5879v2, 2013.

Software Website

 

JIVE: Expresses multiple data matrices on a common set of samples into a sum of low-to-moderate rank matrices capturing joint and individual variation

Joint and Individual Variation Explained (JIVE) for Integrated Analysis of Multiple Datatypes, E.F. Lock, K.A. Hoadley, J.S. Marron and A.B. Nobel, Annals of Applied Statistics, vol.7, 523-542, 2013.

Non-iterative Joint and Individual Variation Explained, Q. Feng, J. Hannig, J.S. Marron, arXiv:1512.04060.

Software Website

 

LAS: Biclustering algorithm that finds significant, large average submatrices in high dimensional data

Finding Large Average Submatrices in high dimensional data, A.A. Shabalin, V.J. Weigman, C.M. Perou and A.B. Nobel, Annals of Applied Statistics, vol.3, pp.985-1012, 2009.

Software Website

 

XDE: Bayesian method for assessing the differential expression of genes using data from multiple studies

A Bayesian model for cross-study differential gene expression (with discussion), R.B. Scharpf, H. Tjelmeland, G. Parmigiani and A.B. Nobel, Journal of the American Statistical Association, vol.104, pp.1295-1310, 2009.

Software Website

 

XPN: Cross-platform normalization method for combining gene expression data from different studies

Merging two gene expression studies via cross platform normalization, A.A. Shabalin, H. Tjelmeland, C. Fan, C.M. Perou and A.B. Nobel, Bioinformatics, vol.24, pp.1154-1160, 2008.

Software Website

 

FastMap: Fast method for performing eQTL analyses in homozygous populations, including permutation based assessment of significance

FastMap: Fast eQTL mapping in homozygous populations, D.M. Gatti, A.A. Shabalin, T-C. Lam, F.A. Wright, I. Rusyn and A.B. Nobel, Bioinformatics, vol.25, pp.482-489, 2008.

Software Website

 

SAFE: Permutation based procedure for assessing the significance of functional categories in gene expression data

Significance analysis of functional categories in gene expression studies: a structured permutation approach, W.T. Barry, A.B. Nobel and F.A. Wright, Bioinformatics, 21:1943-1949, 2005.

Software Website

 

ChIPOTle: Peak finding algorithm for ChIP-chip microarray data

ChIPOTle: A user-friendly tool for the analysis of ChIP-chip data, M.J. Buck, A.B. Nobel and J.D. Lieb, Genome Biology, 6:R97, 2005.

Software Website