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).

Open access (PDF) | Supplement & software | Data

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).

More mode estimation software

Statomics, version 0.4

The Statomics software for empirical Bayes data analysis.