SMASH companion source code repository

Last updated: 2018-12-20

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✔ Repository version: 52a763f

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Unstaged changes:
    Modified:   TODO.txt

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

Expand here to see past versions:

File	Version	Author	Date	Message
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html	99d1f34	Peter Carbonetto	2018-12-07	Re-built all the outdated workflowr webpages.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 and Matthew Stephens (2016). Smoothing via Adaptive Shrinkage (smash): denoising Poisson and heteroskedastic Gaussian signals. arXiv:1709.10066.

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.

The following analyses generate some of the empirical results presented in Xing & Stephens (2016). If you encounter a problem running any of the R code in these examples, please post an issue.

Illustration

SMASH applied to the “Spikes” data set.

Simulation experiments

Illustrative applications

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

The 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 shiny directory contains code to generate the Shiny Web app in R.

License

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.

This reproducible R Markdown analysis was created with workflowr 1.1.1