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Local FDR estimation software

30 June 2012 1 comment

LFDRenrich is a suite of R functions for the estimation of local false discovery rates by maximum likelihood under a two-component or three-component parametric mixture model of 2X2 tables such as those used in gene enrichment analyses.

LFDRhat is a more general suite of R functions for the estimation of local false discovery rates by maximum likelihood under a two-component or three-component parametric mixture model.

Software for local false discovery rate estimation

15 August 2011 Leave a comment

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

9 June 2010 Leave a comment

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

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Significance v. fold change

28 January 2010 Leave a comment

C. M. Yanofsky and D. R. Bickel, “Validation of differential gene expression algorithms: Application comparing fold change estimation to hypothesis testing,” BMC Bioinformatics 11, 63 (2010). Article

Gene network reconstruction from transcriptional dynamics

28 March 2009 Leave a comment

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

5 November 2008 Leave a comment

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.
Categories: software, trainee author