HiCExplorer
HiCExplorer copied to clipboard
deeptools
HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
Hi, I'm trying to run hicCorrelate on my set of 4 raw matrices with a bin size of 500 kb, and keep getting an error "arrays used as indices must...
Hello, I'd like to clarify what "inter-TAD" means in the output from hicInterIntraTAD. Are "inter-TADs" defined as the diamond regions between adjacent TADs?
hello, I have a question on pearson correlation matrix (https://hicexplorer.readthedocs.io/en/latest/content/example_usage.html#a-b-compartment-analysis): how to you calculate the correlation for bewteen 2 loci (such as 100kb) per chromosome? Becasue each locus has only...
Hi, My .cool file contains chrM. For down stream analysis, I need to exclude this. I tried `hicConvertFormat -m s2_1000000.cool --inputFormat cool --outputFormat cool -o s2_1000000woM.cool --chromosome '1', '2', '3',...
I installed in my debian workstation hicexplorer with conda and py37 without any issue. Today I would like to install hicexplorer in my macbook pro m1max with 64gb of RAM,...
**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...
**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 found `hicDifferentialTAD` is quite useful to get differential interactions domains from two matrix. However, I am wondering how to filter the results. The default outputted table is quite...
**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...
Hi, Thank you for the amazing tool. I was wondering if it is possible to compute hicPCA or hicCompartmentalization on matrix with limited interaction range (ex. use interactions between loci...
