Archive
Shrinkage estimation of expression fold change
Z. Montazeri*, C. M. Yanofsky*, and D. R. Bickel, “Shrinkage estimation of effect sizes as an alternative to hypothesis testing followed by estimation in high-dimensional biology: Applications to differential gene expression,” Statistical Applications in Genetics and Molecular Biology 9 (1) 23 (2010). Article | Software
* the first two authors contributed equally
Gene network reconstruction from transcriptional dynamics
D. R. Bickel, Z. Montazeri, P.-C. Hsieh, M. Beatty, S. J. Lawit, and N. J. Bate, “Gene network reconstruction from transcriptional dynamics under kinetic model uncertainty: A case for the second derivative,” Bioinformatics 25, 772-779 (2009).
Local false discovery rate software
Zahra Montazeri and David Bickel developed empiricalBayes, an R software bundle that provides a simple solution to the extreme multiple testing problem. It contains two packages:
- localFDR estimates local false discovery rates given a vector of p-values.
- HighProbability determines which p-values are low enough that their alternative hypotheses can be considered highly probable.
Mode estimation
Paul Poncet’s modeest package implements the half-range mode, the half-sample mode, and the mode-based skewness of D. R. Bickel, “Robust estimators of the mode and skewness of continuous data,” Computational Statistics and Data Analysis 39, 153-163 (2002).
