Software

 

geneSLOPE

Brzyski, D., C. Peterson, E. Candes, M. Bogdan, C. Sabatti, P. Sobczyk (2016) "Controlling the Rate of GWAS False Discoveries"

https://cran.r-project.org/web/packages/geneSLOPE/index.html

TreeQTL

Peterson, C., M. Bogomolov, Y. Benjamini, C. Sabatti (2015) "Hierarchical error control for eQTL studies"

http://www.bioinformatics.org/treeqtl

ptyco

Stell, L. and C. Sabatti (2015) "Genetic variant selection: learning across traits and sites," arXiv:1504.00946

http://web.stanford.edu/~lstell/ptycho/

Piet

Z. Zhang, K. Lange, C. Sabatti (2012) Reconstructing DNA copy number by joint segmentation of multiple sequences

R-Forge Project Home: http://r-forge.r-project.org/projects/piet/

Bayesian sparse hidden components analysis

C. 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

Vocabulon

Sabatti, C. and K. Lange (2002) "Genomewide motif identification using a dictionary model," IEEE Proceedings 90: 1803-1810.

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.

Vocabulon web-site

Volume Measures

Chen, Y., C. Lin, C. Sabatti (2006) "Volume Measures for Linkage Disequilibrium," BMC Genetics 7:54.

Dowload C routines

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