This tool was designed to visualize copy number alterations in single cells. It seamlessly integrates with HiScanner (find our paper here) and allows interactive visualization of HiScanner CNA calls at any resolution.
The tool works out of the box with the visualization output file from HiScanner, which needs to be loaded into the ViScanner website (https://compbio.hms.harvard.edu/ViScanner/). However, you can also use it with your own data (that is not output of HiScanner).
Important: The tool expects a zip-compressed file that contains the following 3 text files:
This file contains bin-level data, meaning each row corresponds to a genomic bin (columns are tab delimited).
Example:
chrom start end major_cn minor_cn total_cn rdr baf cell
1 10027 870642 0 0 0 0.258 0.602 5823PFC-B
1 870643 974114 0 0 0 0.002 0.0 5823PFC-B
1 974115 1080276 0 0 0 0.002 0.0 5823PFC-B
where
- major_cn: major copy number
- minor_cn: minor copy number
- total_cn: total copy number (major_cn + minor_cn)
- rdr: read depth ratio (a measure of the relative read depth in the segment/bin compared to a baseline)
- baf: B allele frequency
- cell: cell identifier
This file contains segment-level data, meaning each row corresponds to a segment (which may span multiple bins) that has the same copy number state (columns are tab delimited).
Example:
chrom start end major_cn minor_cn total_cn rdr baf cell
1 10027 1519210 0 0 0 0.025 0.057 5823PFC-B
1 1519211 1992970 1 0 1 0.378 0.003 5823PFC-B
1 1992971 168586434 1 1 2 1.27 0.431 5823PFC-B
This file contains SNP locations for a specific cell (columns are tab delimited).
Example:
chrom pos 5823PFC-B
1 566870 0.0
1 729679 1.0
1 752566 1.0
In the project directory, you can run:
Runs the app in the development mode.
Open http://localhost:3030 to view it in your browser.
The page will reload when you make changes.
You may also see any lint errors in the console.
Deploys the app on Github pages, so that it is available on https://parklab.github.io/HiScanner/