├── .github └── workflows │ ├── pylint.yml │ ├── python-publish.yml │ └── test.yml ├── .gitignore ├── .readthedocs.yml ├── HiCMatrix_env_ci.yml ├── LICENSE ├── README.rst ├── hicmatrix ├── HiCMatrix.py ├── __init__.py ├── lib │ ├── __init__.py │ ├── cool.py │ ├── ginteractions.py │ ├── h5.py │ ├── hicpro.py │ ├── homer.py │ ├── matrixFile.py │ ├── matrixFileHandler.py │ └── scool.py ├── test │ ├── test_HiCMatrix.py │ ├── test_data │ │ ├── GSE63525_GM12878_insitu_primary_2_5mb_hic2cool042.cool │ │ ├── GSE63525_GM12878_insitu_primary_2_5mb_hic2cool051.cool │ │ ├── Li_et_al_2015.cool │ │ ├── Li_et_al_2015.h5 │ │ ├── one_interaction_4chr.cool │ │ ├── one_interaction_diag_4chr.cool │ │ ├── small_test_matrix.h5 │ │ ├── test_matrix.bed │ │ ├── test_matrix.hicpro │ │ ├── test_matrix.homer │ │ └── test_matrix.homer.gz │ └── test_matrixFileHandler.py └── utilities.py ├── pyproject.toml └── pytest.ini /.github/workflows/pylint.yml: 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