Last updated: 2018-06-22
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Unstaged changes:
Modified: README.md
| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 5567f49 | Peter Carbonetto | 2018-06-22 | wflow_publish(“index.Rmd”) |
| html | 30c6a41 | Peter Carbonetto | 2018-06-21 | Build site. |
| Rmd | f224917 | Peter Carbonetto | 2018-06-21 | wflow_publish(c(“index.Rmd”, “gtexanalysis.Rmd”, “gtexdata.Rmd”)) |
| Rmd | 39d38a8 | Peter Carbonetto | 2018-06-21 | wflow_publish(“index.Rmd”) |
| html | f3feee1 | Peter Carbonetto | 2018-06-21 | Added gtexdata link to home page, and to navbar. |
| Rmd | 3ac4f03 | Peter Carbonetto | 2018-06-21 | wflow_publish(“index.Rmd”) |
| Rmd | e9d1bb2 | Peter Carbonetto | 2018-06-19 | wflow_publish(“index.Rmd”) |
| html | 00b767a | Peter Carbonetto | 2018-06-19 | Made a few small changes to descriptions. |
| Rmd | 08b3e3a | Peter Carbonetto | 2018-06-19 | wflow_publish(“index.Rmd”) |
| html | 3ab329f | Peter Carbonetto | 2018-06-18 | Build site. |
| html | 23c6dda | Peter Carbonetto | 2018-06-04 | More revisions to gtex and index pages. |
| Rmd | f645bba | Peter Carbonetto | 2018-06-04 | wflow_publish(c(“index.Rmd”, “gtex.Rmd”)) |
| html | 03a35cb | Peter Carbonetto | 2018-06-04 | Added “What’s included” section to index. |
| Rmd | b152386 | Peter Carbonetto | 2018-06-04 | wflow_publish(“index.Rmd”) |
| html | 45bcaa8 | Peter Carbonetto | 2018-06-04 | Re-built main webpages after several updates and improvements. |
| Rmd | fe0bcf7 | Peter Carbonetto | 2018-06-04 | wflow_publish(c(“index.Rmd”, “gtex.Rmd”, “fastqtl2mash.Rmd”)) |
| Rmd | 1131043 | Peter Carbonetto | 2018-06-01 | Minor change to homepage. |
| html | fe6f00c | Peter Carbonetto | 2018-06-01 | Fixed links in navbar. |
| Rmd | b82193c | Peter Carbonetto | 2018-06-01 | Moved some output files to data folder; removed some old files from |
| html | 8877b63 | Peter Carbonetto | 2018-06-01 | Moved details of GTEx analysis away from home page. |
| Rmd | ad4ab2a | Peter Carbonetto | 2018-06-01 | wflow_publish(“index.Rmd”) |
| html | be63841 | Peter Carbonetto | 2018-06-01 | More changes to navigation bar. |
| html | b2b5ff9 | Peter Carbonetto | 2018-06-01 | Re-built home page with new navbar. |
| Rmd | eade155 | Peter Carbonetto | 2018-06-01 | wflow_publish(“index.Rmd”) |
| html | f42f07a | Peter Carbonetto | 2018-06-01 | This is a new, pared-down version of the home page. |
| Rmd | 7ec0c30 | Peter Carbonetto | 2018-06-01 | wflow_publish(“index.Rmd”) |
| Rmd | 64caf96 | Peter Carbonetto | 2018-05-31 | Removed most of the materials from the README. |
| Rmd | b98e680 | Gao Wang | 2018-05-31 | Change workflow output folder |
| Rmd | bd0c3fd | Peter Carbonetto | 2018-05-22 | Working on improvements to Fig.GTExExamples.Rmd. |
| Rmd | 2c9e37b | Peter Carbonetto | 2018-05-16 | A few very minor misc. changes. |
| html | 9ce5080 | Peter Carbonetto | 2018-05-14 | Removed R code chunk from index.Rmd. |
| html | abda373 | Peter Carbonetto | 2018-05-14 | Built index.Rmd with new version of workflowr that speeds up |
| Rmd | e7d0e05 | Peter Carbonetto | 2018-05-14 | wflow_publish(“index.Rmd”) |
| Rmd | f4fd799 | Peter Carbonetto | 2018-05-07 | Added step to install packages in instructions (index.Rmd). |
| html | 6206baf | Peter Carbonetto | 2018-05-07 | wflow_publish(“index.Rmd”) took 10 min to complete: |
| Rmd | a58aa04 | Peter Carbonetto | 2018-05-07 | wflow_publish(“index.Rmd”) |
| html | 5c5e02c | Peter Carbonetto | 2018-05-07 | Ran wflow_publish(“index.Rmd”). |
| Rmd | f30f3d6 | Peter Carbonetto | 2018-05-07 | wflow_publish(“index.Rmd”) |
| Rmd | 1668be6 | Peter Carbonetto | 2018-05-07 | Setting up workflowr settings. |
| html | 1668be6 | Peter Carbonetto | 2018-05-07 | Setting up workflowr settings. |
| Rmd | da461d8 | Peter Carbonetto | 2018-05-07 | Added workflowr 1.0.1.9000 files. |
| html | 3c053c7 | Gao Wang | 2017-09-20 | Fix one more broken link |
| html | 094708a | Gao Wang | 2017-09-20 | Update figures |
| html | aecc7f1 | Peter Carbonetto | 2017-09-20 | Moved doc to docs. |
This repository contains code and data resources to accompany our research paper:
Sarah M. Urbut, Gao Wang and Matthew Stephens (2017). Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions. bioRxiv doi:10.1101/096552.
We provide four sets of resources:
If you are primarily interested in applying the multivariate adaptive shrinkage (mash) methods to your own data, please see the mashr R package.
If you would like to obtain the exact GTEx association statistics used in the multivariate adaptive shrinkage (mash) analysis described in our research paper (e.g., so you can apply your method of choice to these data, and compare against our results), please see here.
If you would like follow the exact steps we took to produce the results of the GTEx analysis presented in the manuscript, follow the instructions here. Note: The mashr package was not used in this analysis because mashr was only developed afterward.
If you are working with association statistics from the GTEx study, or similar genetic association data, please see here for our code to convert association statistics in the FastQTL format, or a similar format, to a format that is more suitable for analysis with mash.
If you find any of the source code in this repository useful for your work, please cite our manuscript, Urbut et al (2017). The full citation is given above. Please also cite the Zenodo archive:
Sarah M. Urbut, Gao Wang, Peter Carbonetto and Matthew Stephens (2018), Code and data resources accompanying Urbut et al 2017, version 1.0, Zenodo, doi:10.5281/zenodo.1296399.
Copyright (c) 2016-2018, Sarah Urbut, Gao Wang, Peter Carbonetto and Matthew Stephens.
All source code and software in this repository are made available under the terms of the MIT license.
See here 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”).
This project was developed by Sarah Urbut, Gao Wang, Peter Carbonetto and Matthew Stephens at the University of Chicago.
This reproducible R Markdown analysis was created with workflowr 1.0.1.9000