Last updated: 2018-12-20
workflowr checks: (Click a bullet for more information) ✔ R Markdown file: up-to-date
Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.
✔ Repository version: afcb7cd
wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:
Ignored files:
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Unstaged changes:
Modified: README.md
| File | Version | Author | Date | Message |
|---|---|---|---|---|
| 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| html | 99d1f34 | Peter Carbonetto | 2018-12-07 | Re-built all the outdated workflowr webpages.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.
See [here][gtexresults] for the source repository. This is what you will find in the repository:
├── analysis
├── code
├── data
├── docs
├── output
└── workflowsThe analysis contains R Markdown source files for the workflowr website, including R code used in the final step of the analysis to generate figures and tables for the manuscript.
The code directory contains additional supporting code for the analyses.
The data directory contains original and processed data files used in the mash analysis of the GTEx data, example data sets used to illustrate the data processing and analysis pipelines, and additional data used to generate the tables and figures for the manuscript.
The docs directory contains webpages generated from the R Markdown files in the analysis directory.
The output stores outputs from data processing and analysis pipelines (“workflows”).
The workflows directory contains source code (“SoS workflows”) and Docker configuration files (“Dockerfiles”) implementing a data processing pipeline for mash and an end-to-end analysis of the GTEx data using the multivariate statistical methods (“mash”).
Copyright (c) 2016-2018, 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 waveden, 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.
This reproducible R Markdown analysis was created with workflowr 1.1.1