Last updated: 2018-06-04
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: 4d2da8c
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:
Ignored: .sos/
Ignored: data/.sos/
Ignored: output/MatrixEQTLSumStats.Portable.Z.coved.K3.P3.lite.single.expanded.V1.loglik.rds
Ignored: workflows/.ipynb_checkpoints/
Ignored: workflows/.sos/
Untracked files:
Untracked: fastqtl_to_mash_output/
Untracked: gtex6_workflow_output/
Unstaged changes:
Modified: workflows/README
| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 4d2da8c | Peter Carbonetto | 2018-06-04 | wflow_publish(“index.Rmd”) |
| html | ec7e83e | Peter Carbonetto | 2018-06-04 | Re-built main webpages after several updates and improvements. |
| Rmd | 340ad6f | Peter Carbonetto | 2018-06-04 | wflow_publish(c(“index.Rmd”, “gtex.Rmd”, “fastqtl2mash.Rmd”)) |
| Rmd | bc422e7 | Peter Carbonetto | 2018-06-01 | Minor change to homepage. |
| 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 suitable 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.
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 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 directory is used to store outputs from analysis pipelines.
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