https://github.com/jhrcook/tidy_gtex
The GTEx data in a tidy format for use in R
https://github.com/jhrcook/tidy_gtex
gene-expression gtex r tidy tidyverse tissue
Last synced: about 1 month ago
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The GTEx data in a tidy format for use in R
- Host: GitHub
- URL: https://github.com/jhrcook/tidy_gtex
- Owner: jhrcook
- Created: 2019-05-05T13:48:46.000Z (about 7 years ago)
- Default Branch: master
- Last Pushed: 2019-05-05T17:03:24.000Z (about 7 years ago)
- Last Synced: 2025-03-03T01:15:46.364Z (over 1 year ago)
- Topics: gene-expression, gtex, r, tidy, tidyverse, tissue
- Language: R
- Homepage: https://gtexportal.org/home/
- Size: 5.86 KB
- Stars: 0
- Watchers: 1
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.Rmd
Awesome Lists containing this project
README
---
title: "Tidy GTEx"
author: "Joshua Cook"
date: "2019-05-05"
output: github_document
---
```{r setup, echo=FALSE, message=FALSE, warning=FALSE}
knitr::opts_chunk$set(echo = TRUE, comments = "#>")
library(jhcutils)
library(data.table)
library(magrittr)
library(tidyverse)
```
[](https://github.com/jhrcook)
[](https://twitter.com/JoshDoesa)
[](https://www.joshdoesathing.com)
---
This repository hold the [Genotype-Tissue Expression (GTEx) project](https://gtexportal.org/home/) data in a tidy format for easy use with the R [tidyverse](https://www.tidyverse.org).
> "The Genotype-Tissue Expression (GTEx) project is an ongoing effort to build a comprehensive public resource to study tissue-specific gene expression and regulation. Samples were collected from 53 non-diseased tissue sites across nearly 1000 individuals, primarily for molecular assays including WGS, WES, and RNA-Seq. Remaining samples are available from the GTEx Biobank. The GTEx Portal provides open access to data including gene expression, QTLs, and histology images."
## Data
**Latest download: May 5, 2019**
---
## Git Large File Storage
This repository uses git large file storage ("git-lfs") in order to manage the large data files.
### Installation
The instructions on installing git-lfs for Mac, Windows, and some linux distros are available on the [git-lfs GitHub repo Wiki](https://github.com/git-lfs/git-lfs/wiki/Installation#source). Since I did this work remotely on the HMS Research Computing Cluster, I do not have root access and had to install from source.
1. Download the source code of the latest release from [here](https://github.com/git-lfs/git-lfs/releases/latest).
```bash
wget https://github.com/git-lfs/git-lfs/releases/download/v2.7.2/git-lfs-v2.7.2.tar.gz
```
2. Build the binary using `go build -o /path/to/dest/git-lfs`, where `/path/to/dest/git-lfs` is the name of the directory you store your installed software in. This directory should be in your `$PATH`. For instance, I used `~/bin/git-lfs`.
```bash
module load go
go build -o ~/bin/git-lfs
```
There should now be a file with the same path and name that you passed using the `-o` flag.
3. Set up git-lfs in your git repository.
```bash
cd /path/to/my/git/repo
git lfs install
#> Updated git hooks.
#> Git LFS initialized.
```
4. Declare which files to track.
```bash
git lfs track "*.bigfiles"
#> Tracking "really_big_file.bigfiles"
#> Tracking "so_big_such_wow.bigfiles"
#> Tracking "large_files_rock.bigfiles"
```
where `"*.bigfiles"` is the regular expression for large files in the repo.
5. Track ".gitattributes".
```bash
git add .gitattributes
git commit .gitattributes -m "start git-lfs"
```
You should now be able to add, commit, and push files like normal. Steps 1 and 2 only need to be done once per machine. Steps 3-5 need to be completed once per repository.