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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 |
| Reference manual: | ashr.pdf |
| Vignettes: |
Illustration of Adaptive Shrinkage |
| 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 depends: | mashr |
| Reverse imports: | cytoKernel, debrowser, DiffBind, dreamlet, ebnm, fastTopics, ldsep, limorhyde2, MixTwice, QTLExperiment |
| Reverse suggests: | BindingSiteFinder, dar, DESeq2, flashier, ncvreg, palasso, ribosomeProfilingQC, topconfects |
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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.