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dozmorovlab / multiHiCcompare

Joint normalization of multiple Hi-C matrices, visualization and detection of differential chromatin interactions, supporting covariates.
https://dozmorovlab.github.io/multiHiCcompare/
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Updating straw version #12

Open sa501428 opened 2 years ago

sa501428 commented 2 years ago

Hi!

We've updated straw quite a bit, and specifically, there are new updates in version 9 of the .hic file format that requires using the latest version of straw. In order for users to use this tool with the latest file, ideally the straw version should get updated. Happy to chat if there are questions about this.

StrawR is now also on CRAN. https://cran.r-project.org/web/packages/strawr/

https://github.com/aidenlab/Juicebox/issues/980

mdozmorov commented 2 years ago

Thanks, @sa501428. We currently use the command-line version of straw from https://github.com/theaidenlab/straw/wiki. As long as it works with the latest .hic format, the multiHiCcompare vignette examples should work. @tonyjhlam, if you have any issues, please, let me know. I'll look into using the strawr package in the vignette.