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Software.

Matrix eQTL: Ultra fast eQTL analysis in R/Matlab

Matrix eQTL: Ultra fast eQTL analysis via large matrix operations. A.A. Shabalin Submitted. Software website. Open access PDF at arxiv.org.

LAS: Biclustering algorithm for finding 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, 3(3), 985-1012, 2009. Software webpage. Limited access PDF at AoAS. Open access PDF at arxiv.org.

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, 24(9):1154, 2008. Software webpage. Open access PDF at Bioinformatics.

FastMap: Fast method for eQTL analysis in homozygous populations with 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, 25(4):482, 2009. FastMap 2.0: Fast Association Mapping in Heterozygous Populations D.M. Gatti, A. A. Shabalin, M. Sypa M, T.C. Lam, F.A. Wright, A.B. Nobel, I. Rusyn working paper Software webpage. Open access PDF at Bioinformatics.

SWITCHdna: SupWald Identification of dna-copy Changes

Basal-like Breast Cancer DNA copy number losses identify genes involved in genomic instability, response to therapy, and patient survival. V.J. Weigman, H. H. Chao, A.A. Shabalin, et al. Breast Cancer Research and Treatment, 2 Nov 2011 pp. 1-16. Software webpage.

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