https://github.com/cmdcolin/jbrowse-plugin-ldviewer
https://github.com/cmdcolin/jbrowse-plugin-ldviewer
Last synced: about 1 year ago
JSON representation
- Host: GitHub
- URL: https://github.com/cmdcolin/jbrowse-plugin-ldviewer
- Owner: cmdcolin
- Created: 2025-01-29T00:53:25.000Z (over 1 year ago)
- Default Branch: master
- Last Pushed: 2025-03-15T16:30:16.000Z (over 1 year ago)
- Last Synced: 2025-04-12T19:17:45.395Z (about 1 year ago)
- Language: TypeScript
- Size: 406 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# jbrowse-plugin-ldviewer
A JBrowse 2 plugin for viewing linkage disequilibrium data
Uses a server side plink component
## Screenshot
## Usage
```bash
git clone https://github.com/cmdcolin/jbrowse-plugin-ldviewer
cd jbrowse-plugin-ldviewer
yarn #get main plugin deps
cd ldserver
yarn #get server deps
yarn start #start server, dfault on 4730
```
## Config
This server starts on localhost:4730
If you need to use it on a public server, you can edit your jbrowse config .g.
```json
{
"configuration": {
"LDViewerPlugin": {
"ldserver": "https://yourhost/ldserver"
}
}
}
```
## Future/ideas
The ldserver is a barrier to easy plug-n-play usage of th plugin since it
requires some 'server side admin' (normal jbrowse usage is very client side
focused)
However, I welcome you to try it out!
The server just runs plink2 aka plink 1.9 on some vcf data. I don't know all the
considerations for LD calculations so it may be limited, but gives plausible
results on human 1000g data
We could also consider
- calculating whatever plink is doing on the client side
- if not calculate client sid, we could host ldserver as a public utility, and
set default config to point at it
- support efficient file format like LDmat. it is currently aimed as smallish
regions