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.
Hello， For A / B compartments analysis, I plot the A / B compartments based on the pearson matrix. The pearson matrix was generated by two tools (hicPCA and hicTransform)...
Just a question, is there a way to run hicPCA with a pre-computed obs/exp matrix or a pre-computed pearson matrix? It would be nice to access the PCA functionality directly....
Thanks for the great tools! I would like to run the hicQC on samples that have been merges with hicSumMatrices. These are technical and biological replicates that I processed independently...
[hicInterIntraTAD](https://hicexplorer.readthedocs.io/en/latest/content/tools/hicInterIntraTAD.html) seems to be very useful; however, I immediately ran into the division by zero error. Is it possible to account for such (likely, frequent) events? ```bash ERROR:hicexplorer.hicInterIntraTAD:division by zeroTraceback...
Hi all, i have a bit of a problem when using a modified approach of aligning my Hi-C data with the bwa-mem algorithm. I'm using HiCExplorer version 3.7.2 and python...
Hi, having trouble with the conda install. Specifically: ``` >>conda create --name hicexplorer hicexplorer=3.6 python=3.8 -c bioconda -c conda-forge Collecting package metadata (current_repodata.json): done Solving environment: failed with repodata from...
Thanks a lot for the hicInterIntraTAD function, and one question is whether the calculation of intra-TAD considered the diagonal contacts (self-interacting contacts). Thanks!
Hi, I am using the latest 3.7.2 installed via conda and I am having this error (see below) when executing `hicAdjustMatrix-3.7.2 -a keep --interIntraHandling inter -m matrix.h5 -o matrix.transRemoved.h5 --chromosomes...
I try to use hicConvertFormat to get HicPro format file but something wrong hicConvertFormat --matrices palv_CK_sort.txt.polished.hic.500k_500000.h5 --outFileName palv_CK_sort.txt.polished.hic.500k_500000.hicpro --inputFormat h5 --outputFormat hicpro  I think I'm using it wrong, but...
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