doi:10.1093/biostatistics/kxw041>. These methods can be applied whenever two sets of summary statistics—estimated effects and standard errors—are available, just as 'qvalue' can be applied to previously computed p-values. Two main interfaces are provided: ash(), which is more user-friendly; and ash.workhorse(), which has more options and is geared toward advanced users. The ash() and ash.workhorse() also provides a flexible modeling interface that can accommodate a variety of likelihoods (e.g., normal, Poisson) and mixture priors (e.g., uniform, normal).">

ashr: Methods for Adaptive Shrinkage, using Empirical Bayes (original) (raw)

The R package 'ashr' implements an Empirical Bayes approach for large-scale hypothesis testing and false discovery rate (FDR) estimation based on the methods proposed in M. Stephens, 2016, "False discovery rates: a new deal", <doi:10.1093/biostatistics/kxw041>. These methods can be applied whenever two sets of summary statistics—estimated effects and standard errors—are available, just as 'qvalue' can be applied to previously computed p-values. Two main interfaces are provided: ash(), which is more user-friendly; and ash.workhorse(), which has more options and is geared toward advanced users. The ash() and ash.workhorse() also provides a flexible modeling interface that can accommodate a variety of likelihoods (e.g., normal, Poisson) and mixture priors (e.g., uniform, normal).

Version: 2.2-63
Depends: R (≥ 3.1.0)
Imports: Matrix, stats, graphics, Rcpp (≥ 0.10.5), truncnorm, mixsqp, SQUAREM, etrunct, invgamma
LinkingTo: Rcpp
Suggests: testthat, knitr, rmarkdown, ggplot2, REBayes
Published: 2023-08-21
DOI: 10.32614/CRAN.package.ashr
Author: Matthew Stephens [aut], Peter Carbonetto [aut, cre], Chaoxing Dai [ctb], David Gerard [aut], Mengyin Lu [aut], Lei Sun [aut], Jason Willwerscheid [aut], Nan Xiao [aut], Mazon Zeng [ctb]
Maintainer: Peter Carbonetto
BugReports: https://github.com/stephens999/ashr/issues
License: GPL (≥ 3)
URL: https://github.com/stephens999/ashr
NeedsCompilation: yes
Materials: NEWS
In views: Bayesian
CRAN checks: ashr results

Documentation:

Downloads:

Reverse dependencies:

Reverse depends: mashr
Reverse imports: cytoKernel, debrowser, DiffBind, dreamlet, ebnm, fastTopics, ldsep, limorhyde2, MixTwice, QTLExperiment
Reverse suggests: BindingSiteFinder, dar, DESeq2, flashier, ncvreg, palasso, ribosomeProfilingQC, topconfects

Linking:

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