Last updated: 2019-05-29
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Knit directory: smash-paper/analysis/
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These are the previous versions of the R Markdown and HTML files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view them.
| 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. |
| Rmd | 594f66f | Peter Carbonetto | 2018-12-20 | wflow_publish(“index.Rmd”) |
| 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| html | 99d1f34 | Peter Carbonetto | 2018-12-07 | Re-built all the outdated workflowr webpages. |
| Rmd | 2ddb601 | Peter Carbonetto | 2018-12-06 | I have an initial setup of the Shiny server document. |
| 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. |
| Rmd | 7ebd899 | Peter Carbonetto | 2018-12-04 | wflow_publish(c(“gaussian_signals.Rmd”, “index.Rmd”)) |
| 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 -0.8356286The 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.
See here for the source repository. This is the overall structure of the repository:
├── analysis
├── code
├── data
├── docs
├── dsc
├── output
└── shinyThe analysis directory contains R Markdown source files for the workflowr website, including R code implementing the SMASH demos, and R code to generate tables and figures for the manuscript.
The code directory contains additional supporting code for the demos and analyses of the results.
The data directory contains data files used in the ChIP-seq demo.
The docs directory contains webpages generated from the R Markdown files in the analysis directory.
The dsc directory contains R and MATLAB code used to implement the “Gaussian mean estimation” simulations in the manuscript.
The output directory contains results from the Gaussian and Poisson simulations. The pois_hf.RData file in this directory contains results from experimenting with different Gaussian denoising techniques for the Haar-Fisz algorithm in the Poisson simulations.
The shiny directory contains code to generate the Shiny Web app in R.
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.
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):
[1] workflowr_1.3.0.9000 Rcpp_1.0.1 digest_0.6.17
[4] rprojroot_1.3-2 backports_1.1.2 git2r_0.25.2.9007
[7] magrittr_1.5 evaluate_0.11 stringi_1.2.4
[10] fs_1.2.6 whisker_0.3-2 rmarkdown_1.10
[13] tools_3.4.3 stringr_1.3.1 glue_1.3.0
[16] yaml_2.2.0 compiler_3.4.3 htmltools_0.3.6
[19] knitr_1.20