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.
Hi! Thank you for developing a great suite of tools, and for the excellent documentation.I have a question about calling loops and finding different loops. I have used the commond...
Hi everyone, I noticed an incompatibility issue with cooler 0.9.1. Versions: python 3.10 hicexplorer version 3.7.2 cooler 0.9.1 numpy 1.24.2 Command `hicInfo -m matrix.cool` Output (error) `AttributeError: module 'cooler' has...
Hello, Thanks for creating such a nice tool. I have a bit of a noobish question - I have MicroC data which I have processed via pairtools but I'm stuck...
See https://github.com/deeptools/pyGenomeTracks/issues/443
Duplicate identifiers of reference points (4th column of the annotation bed file) aren`t handled properly by chicAggregateStatistic and the tool crashes, although these entries were automatically relabeled correctly during data...
**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)...
Hi, I am working with human Hi-C data and want to aggregate the signal between PRC2, CTCF, or RAD21 peaks. I only managed to do this plot for PRC2 because...
Hello! Thanks for developing HiCExplorer. Recently I have used hicexplorer (ver 3.7.2) to call TADs, I have Hi-C data and a genome of species A, as well as Hi-C data...
hicConvertFormat -m test.cool -o test.mat --inputFormat cool --outputFormat hicpro -bf test_10000_abs.bed Traceback (most recent call last): File "/home/miniconda3/bin/hicConvertFormat", line 7, in main() File "/home/miniconda3/lib/python3.7/site-packages/hicexplorer/hicConvertFormat.py", line 284, in main matrixFileHandlerOutput.save(args.outFileName[i], pSymmetric=True,...
Hi, I have a query that I am having 2 samples (control.cool and treatment.cool) and ran hicCompareMatrix command and obtained a combined matrix file (combine.cool) and then used hiCPlotMatrix to...
