├── .codecov.yaml ├── .cruft.json ├── .editorconfig ├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.yml │ ├── config.yml │ └── feature_request.yml └── workflows │ ├── build.yaml │ ├── release.yaml │ └── test.yaml ├── .gitignore ├── .pre-commit-config.yaml ├── .readthedocs.yaml ├── CHANGELOG.md ├── LICENSE ├── README.md ├── docs ├── Makefile ├── _static │ ├── .gitkeep │ └── css │ │ └── custom.css ├── _templates │ ├── .gitkeep │ └── autosummary │ │ └── class.rst ├── api.rst ├── changelog.md ├── conf.py ├── contributing.md ├── extensions │ └── typed_returns.py ├── img │ └── infercnv_heatmap.png ├── index.md ├── infercnv.rst ├── notebooks │ ├── .gitignore │ ├── reproduce_infercnv.ipynb │ └── tutorial_3k.ipynb ├── references.bib ├── references.md └── tutorials.rst ├── img ├── infercnv_heatmap.png ├── infercnv_tsne.png └── transcriptome_umap.png ├── pyproject.toml ├── src └── infercnvpy │ ├── __init__.py │ ├── _util.py │ ├── datasets │ ├── __init__.py │ └── data │ │ ├── __init__.py │ │ └── oligodendroglioma.h5ad │ ├── io │ ├── __init__.py │ ├── _genepos.py │ └── _scevan.py │ ├── pl │ ├── __init__.py │ └── _chromosome_heatmap.py │ ├── pp │ └── __init__.py │ └── tl │ ├── __init__.py │ ├── _copykat.py │ ├── _infercnv.py │ └── _scores.py └── tests ├── __init__.py ├── conftest.py ├── data ├── chr1_ensembl.gtf └── chr21_gencode.gtf ├── test_io.py ├── test_plotting.py ├── test_scores.py └── test_tools.py /.codecov.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/icbi-lab/infercnvpy/HEAD/.codecov.yaml -------------------------------------------------------------------------------- /.cruft.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/icbi-lab/infercnvpy/HEAD/.cruft.json -------------------------------------------------------------------------------- /.editorconfig: 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