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: 0.2.50
Depends: R (≥ 3.3.0), ashr (≥ 2.2-22)
Imports: assertthat, utils, stats, plyr, rmeta, Rcpp (≥ 0.12.11), mvtnorm, abind, softImpute
LinkingTo: Rcpp, RcppArmadillo, RcppGSL (≥ 0.3.8)
Suggests: MASS, REBayes, corrplot, testthat, kableExtra, knitr, rmarkdown, profmem, flashr (≥ 0.6.7)
Published: 2021-05-24
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
SystemRequirements: C++11
Additional_repositories: https://stephenslab.github.io/flashr-drat
Citation: mashr citation info
Materials: README
CRAN checks: mashr results

Downloads:

Reference manual: mashr.pdf
Vignettes: using mashr for eQTL studies
EBMN for prior
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
Package source: mashr_0.2.50.tar.gz
Windows binaries: r-devel: mashr_0.2.50.zip, r-devel-UCRT: mashr_0.2.50.zip, r-release: mashr_0.2.50.zip, r-oldrel: mashr_0.2.50.zip
macOS binaries: r-release (arm64): mashr_0.2.50.tgz, r-release (x86_64): mashr_0.2.50.tgz, r-oldrel: mashr_0.2.50.tgz
Old sources: mashr archive

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