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 would like to know if it makes sense to use rnaseq bigwig file in hicpca to flip the signs. For example, choose extra track type --> Histone Mark...
> ERROR:hicexplorer.lib.tadClassifier:Tried to load ML model but failed! Can't get attribute 'LearningWithNoisyLabels' on It was renamed in version 2 of cleanlab https://github.com/cleanlab/cleanlab/releases/tag/v2.0.0 I assume that the models in trained_models/25kb_model_cleanlab_proteins_range.BIN still...
``` Job in error state.. tool_id: hicexplorer_hictraintadclassifier, exit_code: 1, stderr: Fontconfig error: No writable cache directories Traceback (most recent call last): File "/usr/local/bin/hicTrainTADClassifier", line 7, in main() File "/usr/local/lib/python3.10/site-packages/hicexplorer/hicTrainTADClassifier.py", line...
* [ ] Flake8 passes (`flake8 . --exclude=.venv,.build,planemo_test_env,build --ignore=E501,F403,E402,F999,F405,E712`) * [ ] Local tests pass (`py.test hicexplorer --doctest-modules`)
Dear all, I am finding this problem when calculating a background model. Command in: chicQualityControl -m matrix.nr.h5 --referencePoints RFpoints.bed --sparsity 0.025 --threads 20 --outFileName new_RPs.bed chicViewpointBackgroundModel -m matrix.nr.h5 --fixateRange 500000...
Hello, I have 2 cool format files generated by balancing algorithm (hicpro2higlass.sh). I convert them to h5 format, and use hicCompareMatrices to calculate the differences between 2 matrices with h5...
Hi, I downloaded the new version of HiCExplorer with conda and then also did: git clone https://github.com/deeptools/HiCExplorer/ cd HiCExplorer git checkout aggregateGenome hicex_git_dir=$(pwd) export PATH=$hicex_git_dir/bin:$PATH export PYTHONPATH=$hicex_git_dir:$PYTHONPATH but the aggreateGenome...
Hi everyone, I'm trying to use the hicPCA command but I get an error message: ``` $ hicPCA -m mat_160K_corrected.cool --outputFileName pca1.bw pca2.bw pca3.bw --format bigwig Traceback (most recent call...
Hello, I was wondering if the aligned bam file from bwa needs to be sorted or can we directly input it into hicBuildMatrix. Thank you
hello! I use this command to generate the hic matrix :hicBuildMatrix --samFiles mate_R1_sorted.bam mate_R2_sorted.bam \ --binSize 10000 \ --restrictionSequence GATC \ --threads 8 \ --inputBufferSize 1000000000 \ --outBam hic.bam \...
