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Calculating intra/inter-TAD interactions #404

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ywiwasaki opened this issue Jun 28, 2019 · 3 comments
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Calculating intra/inter-TAD interactions #404

ywiwasaki opened this issue Jun 28, 2019 · 3 comments
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Feature request implemented in develop

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@ywiwasaki
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I want to calculate density of intra-TAD interactions and inter-TAD interactions for each of the TADs defined by HiCExplorer. Is there any way to do this using HiCExplorer? (Or do I need to calculate it by using the matrix file converted in ginteractions format?)
@joachimwolff
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Hi,

Sorry, this feature we do not have currently in HiCExplorer.

Best,

Joachim

@joachimwolff joachimwolff reopened this Jul 6, 2019
@LeilyR LeilyR mentioned this issue May 18, 2020
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@Drosophilid
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Hi,

I also got stuck with a similar situation to calculate the Inter vs Intra TAD interactions. Would it be possible to do it now in the recent release?

Any kind of help or suggestion will be appreciated.

Thanks

joachimwolff added a commit that referenced this issue Jul 8, 2021
@joachimwolff
First implementation of inter and intra tad computations, feature req…
e00b13f 
…uest #404
joachimwolff added a commit that referenced this issue Jul 9, 2021
@joachimwolff
Adding test data for hicInterIntraTAD, fixing density calculation, ad…
32add8c 
…ding option to plot ratio. Adding test case for hicInterIntraTAD. #404
@joachimwolff
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Implemented with PR #733.

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@joachimwolff @ywiwasaki @Drosophilid