CHARM
Documentation
CHARM
Comprehensive Hub of Alternative Regulatory Mapping
RNA-binding protein expression, splicing, and eCLIP binding data. Available as a web app, or as a local pipeline you can run and extend yourself. Pick the guide that matches what you want to do.
No code required
CHARM App Tutorial
Explore RNA-binding protein expression, splicing, and eCLIP binding data through the CHARM Shiny web app. Browse ENCODE reference data, upload your own results in Discovery mode, and observe potential multi-omic RBP networks, all in your browser.
Command line · R & Python
eCLIPSE Local Pipeline
Run the eCLIPSE pipeline yourself outside the app. Build your own splicing genome from VAST-TOOLS/VastDB, rMATS or other event-centered tools, intersect it with your own eCLIP peaks, and generate RNA binding maps.
Not sure which one you need? If you just want to look up an RBP's expression, splicing, or binding data, start with the App Tutorial. If you have your own eCLIP or splicing data and want to build binding maps locally, start with the eCLIPSE Local Pipeline guide.