https://github.com/jackhump/sqtlviztools
functions for sQTL visualisation
https://github.com/jackhump/sqtlviztools
Last synced: 5 months ago
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functions for sQTL visualisation
- Host: GitHub
- URL: https://github.com/jackhump/sqtlviztools
- Owner: jackhump
- License: other
- Created: 2017-12-15T12:33:02.000Z (over 8 years ago)
- Default Branch: master
- Last Pushed: 2021-02-23T16:33:43.000Z (over 5 years ago)
- Last Synced: 2023-10-20T20:31:59.644Z (over 2 years ago)
- Language: R
- Size: 3.87 MB
- Stars: 4
- Watchers: 2
- Forks: 2
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# sQTLviztools
An R package and associated scripts for visualisation splicing quantitative trait loci (sQTLs).
## Citing sQTLviztools
If you use sQTLviztools in your work, please cite the following two papers:
- https://www.nature.com/articles/s41588-018-0238-1
- https://www.nature.com/articles/s41467-019-08912-9
## Installation
1. clone the sqtlviztools repo
```
git clone https://github.com/jackhump/sqtlviztools.git
```
2. install the R package and any dependencies
in R:
```{r}
install.packages("remotes")
remotes::install_github("jackhump/sQTLviztools")
```
# Running the example data
I picked a SNP / intron cluster pair at random from the ROSMAP shiny app - https://rajlab.shinyapps.io/sQTLviz_ROSMAP/
In the examples folder there is a toy version of each file you'll need to visualise sQTLs.
1. Create the example Rdata file
on the command line:
```
cd sqtlviztools/
Rscript prepare_example.R
```
2. Run the example Shiny app
```
cd shiny/
Rscript shiny/run_shiny.R
```
Please raise an issue on this github if you can't get the example app working.