HiCExplorer
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deeptools
HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
In the documentation, under Example Usage, is the page "Importing and Exporting HiCExplorer data". I was able to follow the example up until the step of converting the .tsv file...
Currently using version 3.7.2. When I use `--log1p` and `--vMin/--vMax` simultaneously it returns the following error (that i imagine comes from matplotlib, in my case: matplotlib-base ==3.5.1, matplotlib-inline==0.1.3) My command:...
hello, i used conda to install hicexplorer in a new environment, but i can't use hicDetectLoops or hicHyperoptDetectLoops, $ hicDetectLoops -h Traceback (most recent call last): File "/data/jerry/software/miniconda3/envs/hicexplorer/bin/hicDetectLoops", line 4,...
It appears that the current HiCExplorer is not compatible with python 3.10. The issue looks to be related to the 'collections' module import syntax: `Traceback (most recent call last): File...
Hello, would you like to tell me that hicConvertFormat can convert HiC-Pro **iced matrix** to cool or other formats? hicConvertFormat -m fastq_100000_iced.matrix --bedFileHicpro ${bed} --resolutions 100000 --inputFormat hicpro --outputFormat cool...
- HiCExplorer version == 3.7.2 (installed using conda) - Python version == 3.9.13 Hi there, I'm observing a weird behavior of the HicConvertFormat function, when I'm using a 2d-text bed...
Hello, I am having problems using .hic files generated using Juicer v2.0 Specifically: UnicodeDecodeError: 'utf-8' codec can't decode byte 0xaf in position 1: invalid start byte This could possibly be...
Dear Developers, I'm trying to generate compiled 3C-like profiles for a tRNA and I encountered the following error message: chicViewpointBackgroundModel --matrices CTR.h5 T1.h5 T2.h5 --referencePoints reference_point.bed --outFileName background_model.bed chicViewpoint --matrices...
Hi, I got a error as below: ERROR:hicexplorer.iterativeCorrection:*Error* matrix correction produced extremely large values. This is often caused by bins of low counts. Use a more stringent filtering of bins....
Hi, I'm recently using HiCExplorer to analyze my Hi-C data. First, thank you for the fantastic tool for researchers to use! :) I have a question using the hicInterIntraTAD tool...
