Last updated: 2018-06-01
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 6a456e6 | Peter Carbonetto | 2018-06-01 | Moved some output files to data folder; removed some old files from |
| html | 165554d | Peter Carbonetto | 2018-06-01 | Moved details of GTEx analysis away from home page. |
| Rmd | 7e3cfc7 | Peter Carbonetto | 2018-06-01 | wflow_publish(“index.Rmd”) |
| html | da644a1 | Peter Carbonetto | 2018-06-01 | Re-built home page with new navbar. |
| Rmd | 515985c | Peter Carbonetto | 2018-06-01 | wflow_publish(“index.Rmd”) |
| html | dad17f3 | Peter Carbonetto | 2018-06-01 | This is a new, pared-down version of the home page. |
| Rmd | fbc54f1 | Peter Carbonetto | 2018-06-01 | wflow_publish(“index.Rmd”) |
| Rmd | 2945c3d | Peter Carbonetto | 2018-05-31 | Removed most of the materials from the README. |
| Rmd | bd60ada | Gao Wang | 2018-05-31 | Change workflow output folder |
| Rmd | 380046f | Peter Carbonetto | 2018-05-22 | Working on improvements to Fig.GTExExamples.Rmd. |
| Rmd | d9994cf | Peter Carbonetto | 2018-05-16 | A few very minor misc. changes. |
| Rmd | 3431f02 | Peter Carbonetto | 2018-05-14 | wflow_publish(“index.Rmd”) |
| Rmd | ea42e8a | Peter Carbonetto | 2018-05-07 | Added step to install packages in instructions (index.Rmd). |
| Rmd | 6ebb3f9 | Peter Carbonetto | 2018-05-07 | wflow_publish(“index.Rmd”) |
| Rmd | c6c8450 | Peter Carbonetto | 2018-05-07 | Setting up workflowr settings. |
| html | c6c8450 | Peter Carbonetto | 2018-05-07 | Setting up workflowr settings. |
| Rmd | 33f72d6 | Peter Carbonetto | 2018-05-07 | Added workflowr 1.0.1.9000 files. |
| html | b4e38c2 | Gao Wang | 2017-09-20 | Fix one more broken link |
| html | 80f285f | Gao Wang | 2017-09-20 | Update figures |
| html | afc401f | Peter Carbonetto | 2017-09-20 | Moved doc to docs. |
This repository contains code 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 three sets of code resources:
If you are primarily interested in applying the multivariate adaptive shrinkage (mash) methods to your own data, please see the mashr repository.
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 convenient for analysis with mashr.
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.
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.
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.
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This project was developed by Sarah Urbut, Gao Wang, Peter Carbonetto. Matthew Stephens at the University of Chicago.
This reproducible R Markdown analysis was created with workflowr 1.0.1.9000