Ruth Heller

R Packages:

• HHG

  • Description: A nonparametric test of independence between two random vectors based on distances described here. Also, the distribution free univariate K-sample and independence tests described here.
  • Download:from CRAN repository .
  • Related papers: A consistent multivariate test of association based on ranks of distances,Consistent distribution-free tests of association between univariate random variables.
  • Tables of null distributions: DIRECTORY.

• repfdr

  • Description: Estimation of Bayes and local Bayes false discovery rates for replicability analysis.
  • Download: from CRAN repository.
  • Related paper: Replicability analysis for genome-wide association studies,repfdr: A tool for replicability analysis for genome-wide association studies.

• Crossmatch

  • Description: This package performs a test for comparing two multivariate distributions by using the distance between observations. The input is a distance matrix and the labels of the two groups to be compared, the output is the number of cross-matches and a p-value.
  • Download: from CRAN repository.
  • Related paper:
    Rosenbaum, P.R. (2005),
    An exact distribution-free test comparing two multivariate distributions based on adjacency
    Journal of the Royal Statistical Society: Series B (Statistical Methodology), 67, 4, 515-530.

Web Applet

• ReplicabilityFDR

  • Description: Computation of the FDR r-values for the primary to follow-up design. The FDR r-value for a feature is the smallest FDR level q at which we can say that the finding is among the replicated ones.
  • URL: Web Applet in link.
  • Download: R code in link.
  • Related paper: Deciding whether follow-up studies have replicated findings in a preliminary large-scale ``omics' study"

Script Files

• ReplicabilityFDR

  • Download: R code in .txt file.
  • Related paper: Deciding whether follow-up studies have replicated findings in a preliminary large-scale ``omics' study"

• A Flexible 2 Stage Procedure for Identifying Gene Sets that are Differentially Expressed

  • Download: R code in .txt file.
  • Related paper: A Flexible 2 Stage Procedure for Identifying Gene Sets that are Differentially Expressed

• Matching methods for observational microarray studies

  • Download: R code in .txt file.
  • Related paper: Matching methods for observational microarray studies

• Screening for partial conjunction hypotheses

  • Download: Matlab code in .RAR file.
  • Related paper: Screening for partial conjunction hypotheses

• Cluster Based Analysis of FMRI Data

  • Download: Matlab code in .RAR file.
  • Related paper: Cluster-based analysis of FMRI data