Software  
geneSLOPEBrzyski, D., C. Peterson, E. Candes, M. Bogdan, C. Sabatti, P. Sobczyk (2016) "Controlling the Rate of GWAS False Discoveries" https://cran.rproject.org/web/packages/geneSLOPE/index.htmlTreeQTLPeterson, C., M. Bogomolov, Y. Benjamini, C. Sabatti (2015) "Hierarchical error control for eQTL studies" http://www.bioinformatics.org/treeqtlptycoStell, L. and C. Sabatti (2015) "Genetic variant selection: learning across traits and sites," arXiv:1504.00946 http://web.stanford.edu/~lstell/ptycho/PietZ. Zhang, K. Lange, C. Sabatti (2012) Reconstructing DNA copy number by joint segmentation of multiple sequences RForge Project Home: http://rforge.rproject.org/projects/piet/Bayesian sparse hidden components analysisC. Sabatti and G. James "Bayesian sparse hidden components analysis for transcription regulation networks" Bioinformatics, Advance Access published on December 20, 2005 Text file containing an R function that samples from the posterior distribution of A,P,Z: BNCA.R Note that to perform the transcription network reconstruction described in the article, you need to have a prior probability on Z, derived from sequence analysis. In Sabatti and James (2005) we use the Vocabulon algorithm with this goal. The R Project for Statistical Computing VocabulonSabatti, C. and K. Lange (2002) "Genomewide motif identification using a dictionary model," IEEE Proceedings 90: 18031810. Sabatti, C., L. Rohlin, K. Lange, and J. C. Liao (2005) "Vocabulon: a dictionary model approach for reconstruction and localization of transcription factor binding sites" Bioinformatics, 21: 922  931. Volume MeasuresChen, Y., C. Lin, C. Sabatti (2006) "Volume Measures for Linkage Disequilibrium," BMC Genetics 7:54. 

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