Last updated: 2019-05-29

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Knit directory: smash-paper/analysis/

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File Version Author Date Message
Rmd d787b97 Peter Carbonetto 2019-05-29 wflow_publish(“analysis/index.Rmd”)
Rmd b9f5cd3 Peter Carbonetto 2018-12-21 wflow_publish(c(“index.Rmd”, “poisson.Rmd”))
html c815163 Peter Carbonetto 2018-12-20 Added info about Poisson results in output directory.
Rmd 840ef19 Peter Carbonetto 2018-12-20 wflow_publish(“index.Rmd”)
html 7dc40a9 Peter Carbonetto 2018-12-20 Revised license info given in home page.
Rmd 52a763f Peter Carbonetto 2018-12-20 wflow_publish(“index.Rmd”)
html 92215ee Peter Carbonetto 2018-12-20 Revised “what’s included” section.
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Rmd afcb7cd Peter Carbonetto 2018-12-20 wflow_publish(“index.Rmd”)
html 24792c7 Peter Carbonetto 2018-12-20 Added link to poisson page in the home page.
Rmd 13aafbf Peter Carbonetto 2018-12-20 wflow_publish(“index.Rmd”)
html 99d1f34 Peter Carbonetto 2018-12-07 Re-built all the outdated workflowr webpages.
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Rmd c589dbb Peter Carbonetto 2018-12-06 wflow_publish(c(“index.Rmd”, “gaussian_signals.Rmd”,
Rmd d82c55d Peter Carbonetto 2018-12-04 Added shiny page to home.
Rmd ef0b2de Peter Carbonetto 2018-12-04 Minor edits to home page.
html 35f03c0 Peter Carbonetto 2018-12-04 Changed title of gaussian_signals.Rmd.
Rmd 4a35339 Peter Carbonetto 2018-12-04 wflow_publish(c(“gaussian_signals.Rmd”, “index.Rmd”))
html 6897465 Peter Carbonetto 2018-12-04 Added gaussian_signals page to the home.
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Rmd 049dcbb Peter Carbonetto 2018-11-08 Moved around some files and revised TOC in home page.
Rmd 1b61bd1 Peter Carbonetto 2018-11-08 wflow_publish(“index.Rmd”)
Rmd 58539f5 Peter Carbonetto 2018-11-08 wflow_publish(“index.Rmd”)
Rmd f4372ca Peter Carbonetto 2018-11-08 Moved around some of the files, and revising the home page.
html b5453fa Peter Carbonetto 2018-11-06 Small edit to home page.
html 4c88a8b Peter Carbonetto 2018-11-06 A few more fixes to the home page.
Rmd 7caace6 Peter Carbonetto 2018-11-06 wflow_publish(“index.Rmd”)
Rmd 4baa137 Peter Carbonetto 2018-11-06 wflow_publish(“index.Rmd”)
html 0328612 Peter Carbonetto 2018-11-06 Re-built the home page after revamping it.
Rmd aa4437d Peter Carbonetto 2018-11-06 wflow_publish(“index.Rmd”)
Rmd 27bb547 Peter Carbonetto 2018-11-06 Greatly simplified the README.
html 0a6b926 Peter Carbonetto 2018-10-18 Adjusted workflowr site rendering.
html c0faf17 Peter Carbonetto 2018-10-18 Added links to analyses in home page.
Rmd 40ad2f2 Peter Carbonetto 2018-10-18 wflow_publish(“index.Rmd”)
html 0797696 Peter Carbonetto 2018-08-23 Build site.
Rmd 80e51ae Peter Carbonetto 2018-08-23 Start workflowr project with wflow_start().

This repository contains data and R source code accompanying our manuscript,

Zhengrong Xing, Peter Carbonetto and Matthew Stephens (2019). Flexible signal denoising via flexible empirical Bayes shrinkage. arXiv:1605.07787.

If you find any of the source code in this repository useful for your work, please cite our paper.

The new methods can be found in the smashr package.

rnorm(3)
[1] -0.6264538  0.1836433 -0.8356286

Contents

The following analyses generate some of the empirical results presented in Xing, Carbonetto & Stephens (2019). If you encounter a problem running any of the R code in these examples, please post an issue.

Illustrative applications

  1. Motorcycle acceleration data.

  2. ChIP-seq data.

What’s included in the git repository

See here for the source repository. This is the overall structure of the repository:

├── analysis
├── code
├── data
├── docs
├── dsc
├── output
└── shiny

License

Copyright (c) 2016-2019, Zhengrong Xing, Peter Carbonetto & Matthew Stephens.

Our numerical comparisons make use of some of the functions from WaveLab, so we have included the WaveLab source code in this repository. See the COPYING.m Wavelab850 subdirectory for more information about distributing WaveLab.

Our numerical comparisons also use of some functions from GaussianWaveDen, so we have included the GaussianWaveDen source in this repository. For information about distributing GaussianWaveDen, see the copyright.m in the WavDen subdirectory. Note that we made one small improvement to the code in blockJS.m to prevent an error that occurs when running the code in newer versions of MATLAB.

All other source code and software in this repository are made available under the terms of the MIT license. See the LICENSE file in the git repository for the full text of the license.

Credits

This project was developed by Zhengrong Xing at the University of Chicago, with support and contributions from Peter Carbonetto and Matthew Stephens.


sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
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