HiCExplorer

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Suggestion - Zscore transformation a la hicFindTADs

1

Hi, I find the Z-score transformation performed by hicFindTADs very useful for quantitative analysis of contact enrichment. I think it would be nice to add this way of transforming the...

samuelCollombet

Hi, I have analyzed my hi-c data using TADCompare(), it outputs a data frame with the following data Boundary | Gap_Score | TAD_Score1 | TAD_Score2 | Differential | Enriched_In |...

MurliNair

UnicodeDecodeError When running hicConvertFormat to convert HiC to Cool format

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**Welcome to the HiCExplorer GitHub repository! Before opening the issue please check that the following requirements are met :** - [ ] Search whether this issue (or a similar issue)...

ashishjain1988

Have you considered the ability to add multiple threads, which is really slow when the matrix is large.

wbszhu

**Welcome to the HiCExplorer GitHub repository! Before opening the issue please check that the following requirements are met :** - [x] Search whether this issue (or a similar issue) has...

biofilos

` hicCorrectMatrix correct` issue

1

Hi, I have several questions relevant to `hicCorrectMatrix correct`. 1. The coverage histogram of my data showed that the count bins are not well distributed and didn't strictly follow the...

PanZiwei

Hi, I encountered an error `OSError: 'GSM2644945_Untreated-R1.100000_chr1.cool' is not an HDF5 file.` when running the `hicDifferentialTAD` function with the test dataset in `.cool` format you showed in the readme file....

PanZiwei

resolution hicPlotTADs

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Hi! I'm still working with hicexplorer and i have questions about plot. I can't succeed to plot nice and clean plot. I don't know if it's because i didn't produce...

MarineBergot

problem with hicAggragateContacts

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Version 3.7.2 Good morning, I'm using hicAggregateContacts for creating new plots, I've used this command in previously ocasions and I didn't have any trouble, now I'm using a matrix of...

eferreA9

Hello FYI while trying to install HiCEplorer version 3.7.3 (from release archive) using the described method in README, ie: `python setup.py install` I have the following error message. ``` /opt/gensoft/exe/HiCExplorer/3.7.3/venv/lib/python3.10/site-packages/setuptools/command/build_py.py:207:...

EricDeveaud