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my hicexploer is in v 3.5 and python in 3.7.8.
when using hicCorrelation on cooler files, it turns out that dtype of all_nan array is float instead of int/bool, so the remove nan process cannot be d…
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Thanks for providing this efficient tool.
I wonder is it possible to plot aggregated Hi-C sub-matrices of a specified list of positions, such as sub-contacts around some histone peaks?
similar …
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Hi,
I just noticed that if you use hicFindTADs with a cool matrix, then the zscore_matrix is ending with `h5` but it is a `cool` file:
https://github.com/deeptools/HiCExplorer/blob/22b731cfd537a38e8…
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Just need clarification:
in hicPlotMatrix, by default, it applies correction (* weight) on the matrix? And in hicCorrelate, by default, it doesn't apply such correction?
And I think maybe some times…
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When I use `hicPlotMatrix --bigwig PC1.bw` without `--clearMaskedBins` to plot a Hi-C matrix and its A/B compartment track, the position of the bw track is not correct. This only happens when the star…
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Hi, I'm using hicFindTADs version 3.4.1 and am using the following commands to try to call TADs. The input data is a cooler with a resolution of 500bp.
```
cooler balance --cis-only thirteen_scafs…
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Thank you for maintaining and continuously improving this great library! I'm now attempting to generate some figures involving Hi-C and has run into a few minor hiccups.
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All of our data are st…
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_Commit_: Recent
Hi,
I am trying to visualize a multicooler with HiGlass including addition of the search position. For this we first generated contact matrices with HiCExplorer (https://hicexpl…
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Hi,
I have successfully run HiCExplorer for my datasets. The output of the matrix file is in .h5 format and I have converted in different formats by hicconvert program.
**I am looking for a Normal…