mashr: Multivariate Adaptive Shrinkage in R

Travis Build Status codecov

This package implements methods to estimate and test many effects in many conditions (or many effects on many outcomes).

Empirical Bayes methods are used to estimate patterns of similarity among conditions, then exploit these patterns of similarity among conditions to improve accuracy of effect estimates. See Urbut et al for details.

Note: the R package used to generate the results for the manuscript is here.

Quick Start

  1. Follow the setup instructions below.

  2. See the introductory vignette for an introduction to mashr.

  3. Then walk through these vignettes to learn more about mashr: Introduction to mash: data-driven covariances and Simulation with non-canonical matrices.

Citing this work

If you find the masr package or any of the source code in this repository useful for your work, please cite:

Sarah Urbut, Gao Wang, Peter Carbonetto and Matthew Stephens (2019). Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions. Nature Genetics 51, 187-195.


Please follow these steps to install mashr.

  1. Unlike most packages available on CRAN, mashr is not precompiled, and therefore to install mashr you will need to make sure that your R installation is properly set up to compile packages with C++ source; in particular, the C++ compiler programs supported by your version of R should be installed on your computer, and R should be correctly configured to call these compilers when installing packages from source. For more information, see the CRAN documentation.

  2. Install the latest release of the mashr package using devtools:


    This command should automatically install any missing dependencies that are available from CRAN. This command should also automatically retrieve and install the latest version of the ashr package from Github. If it does not, you can install the ashr package separately using devtools:

  3. By default, the devtools::install_github function does not build the vignettes. If you would like to build the vignettes as well, you will need to several additional packages, including flashr, that are used only in the vignettes. This can also be done with devtools:

    devtools::install_github("stephenslab/mashr@v0.2-11",dependencies = TRUE,
                             build_vignettes = TRUE)

Developer notes