Archive
Software for estimating the local false discovery rate
R functions for combining probabilities using game theory
Suite of R functions for combination of probabilities using a game-theoretic method
R package for estimating local false discovery rates using empirical Bayes methods
LFDREmpiricalBayes — Estimating Local False Discovery Rates Using Empirical Bayes Methods
An R package to transform false discovery rates to posterior probability estimates
There are many estimators of false discovery rate. In this package we compute the Nonlocal False Discovery Rate (NFDR) and the estimators of local false discovery rate: Corrected False discovery Rate (CFDR), Re-ranked False Discovery rate (RFDR) and the blended estimator.
Source: CRAN – Package CorrectedFDR
LFDR.MLE-package function | R Documentation
Suite of R functions for the estimation of the local false discovery rate (LFDR) using Type II maximum likelihood estimation (MLE):
Empirical Bayes software (R packages)
Empirical Bayes software packages:
Software for local false discovery rate estimation
LFDR-MLE is a suite of R functions for the estimation of local false discovery rates by maximum likelihood under a two-group parametric mixture model of test statistics.
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).
David Bickel, statistician 
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