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SegmentModel Spy

DOI

SegmentModel Spy is a an interactive visualization tool for GATK's copy-number segmentation results. In practice, it does (almost) all that PlotModeledSegments does but adds continuous panning and zooming and provides a few annotation tracks. Under the hood, SegmentModel Spy uses GenomeSpy for WebGL-based rendering. This tool is also an example of how to use GenomeSpy in a web application.

An online version is available at https://genomespy.app/segmentmodel/

Local installation (for development)

  1. git clone [email protected]:genome-spy/segment-model-spy.git
  2. cd segment-model-spy
  3. npm install
  4. npm start
  5. Browse to http://localhost:5173/ or whatever port is shown on the console.

Legal stuff and acknowledgements

Copyright (c) 2020-2024 Kari Lavikka. See LICENSE for details.

SegmentModel Spy is developed in The Systems Biology of Drug Resistance in Cancer group at the University of Helsinki.

This project has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No. 965193 (DECIDER) and No. 847912 (RESCUER), the Sigrid Jusélius Foundation and the Cancer Foundation Finland.

GATK is a trademark of the Broad Institute, Inc.