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mashr: Multivariate Adaptive Shrinkage

Implements the multivariate adaptive shrinkage (mash) method of Urbut et al (2019) <doi:10.1038/s41588-018-0268-8> for estimating and testing large numbers of effects in many conditions (or many outcomes). Mash takes an empirical Bayes approach to testing and effect estimation; it estimates patterns of similarity among conditions, then exploits these patterns to improve accuracy of the effect estimates. The core linear algebra is implemented in C++ for fast model fitting and posterior computation.

Version: 0.2.79
Depends: R (≥ 3.3.0), ashr (≥ 2.2-22)
Imports: assertthat, utils, stats, plyr, rmeta, Rcpp (≥ 1.0.8), mvtnorm, abind, softImpute
LinkingTo: Rcpp, RcppArmadillo, RcppGSL (≥ 0.3.8)
Suggests: MASS, REBayes, corrplot (≥ 0.90), testthat, kableExtra, knitr, rmarkdown, profmem, flashier, ebnm
Published: 2023-10-18
DOI: 10.32614/CRAN.package.mashr
Author: Matthew Stephens [aut], Sarah Urbut [aut], Gao Wang [aut], Yuxin Zou [aut], Yunqi Yang [ctb], Sam Roweis [cph], David Hogg [cph], Jo Bovy [cph], Peter Carbonetto [aut, cre]
Maintainer: Peter Carbonetto <peter.carbonetto at gmail.com>
BugReports: https://github.com/stephenslab/mashr/issues
License: BSD_3_clause + file LICENSE
Copyright: file COPYRIGHTS
mashr copyright details
URL: https://github.com/stephenslab/mashr
NeedsCompilation: yes
Citation: mashr citation info
Materials: README
CRAN checks: mashr results

Documentation:

Reference manual: mashr.pdf
Vignettes: using mashr for eQTL studies
mashr intro with correlations
mashr intro with data-driven covariances
mashr intro
mashnocommonbaseline intro
mashcommonbaseline intro
Sample from mash posteriors
mashr simulation with non-canonical matrices

Downloads:

Package source: mashr_0.2.79.tar.gz
Windows binaries: r-devel: mashr_0.2.79.zip, r-release: mashr_0.2.79.zip, r-oldrel: mashr_0.2.79.zip
macOS binaries: r-release (arm64): mashr_0.2.79.tgz, r-oldrel (arm64): mashr_0.2.79.tgz, r-release (x86_64): mashr_0.2.79.tgz, r-oldrel (x86_64): mashr_0.2.79.tgz
Old sources: mashr archive

Reverse dependencies:

Reverse imports: dreamlet, limorhyde2, multistateQTL

Linking:

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

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.
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