ashr: Methods for Adaptive Shrinkage, using Empirical Bayes

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 <pcarbo at uchicago.edu>
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:

Reference manual:	ashr.html , ashr.pdf
Vignettes:	Illustration of Adaptive Shrinkage (source, R code)

Downloads:

Package source:	ashr_2.2-63.tar.gz
Windows binaries:	r-devel: ashr_2.2-63.zip, r-release: ashr_2.2-63.zip, r-oldrel: ashr_2.2-63.zip
macOS binaries:	r-release (arm64): ashr_2.2-63.tgz, r-oldrel (arm64): ashr_2.2-63.tgz, r-release (x86_64): ashr_2.2-63.tgz, r-oldrel (x86_64): ashr_2.2-63.tgz
Old sources:	ashr archive

Reverse dependencies:

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

Linking:

Please use the canonical form https://CRAN.R-project.org/package=ashr to link to this page.