├── .coveragerc ├── .gitattributes ├── .github └── images │ └── imaging_transcriptomics.png ├── .gitignore ├── LICENSE ├── MANIFEST.in ├── README.md ├── docs ├── .vscode │ └── settings.json ├── Makefile ├── chapters │ ├── 01_getting_started.rst │ ├── 02_theory.rst │ ├── 03_installation.rst │ ├── 04_usage.rst │ ├── 05_what_to_do.rst │ ├── 06_contributing.rst │ ├── 07_contact_us.rst │ ├── 08_faq.rst │ └── images │ │ ├── dk_atlas.jpg │ │ └── imaging_transcriptomics.png ├── conf.py ├── index.rst ├── make.bat └── requirements.txt ├── environment.yml ├── imaging_transcriptomics ├── __init__.py ├── corr.py ├── data │ ├── atlases │ │ ├── DK │ │ │ ├── atlas-DK_1mm.nii.gz │ │ │ ├── atlas-DK_2mm.nii.gz │ │ │ ├── atlas-DK_fsa5_lh_aparc.annot │ │ │ ├── atlas-DK_fsa5_rh_aparc.annot │ │ │ ├── atlas-DK_gene_expression_data.csv │ │ │ ├── atlas-DK_gene_expression_labels.txt │ │ │ └── atlas-DK_labels.csv │ │ └── Schaefer_100 │ │ │ ├── atlas-Schaefer_100_1mm.nii.gz │ │ │ ├── atlas-Schaefer_100_2mm.nii.gz │ │ │ ├── atlas-Schaefer_100_gene_expression_data.csv │ │ │ ├── atlas-Schaefer_100_labels.csv │ │ │ ├── atlas-Schaefer_100_lh_aparc.annot │ │ │ └── atlas-Schaefer_100_rh_aparc.annot │ ├── geneset_LAKE.gmt │ └── geneset_Pooled.gmt ├── errors.py ├── genes.py ├── inputs.py ├── log_config.yaml ├── pls.py ├── reporting.py ├── resources │ ├── Header_final.pdf │ ├── header.png │ ├── header.svg │ └── order_enigma.csv ├── script │ ├── __init__.py │ ├── imagingtranscriptomics.py │ ├── imt_gsea.py │ └── log_config.yaml ├── tests │ ├── __init__.py │ ├── auto_test.py │ ├── conftest.py │ ├── data │ │ ├── MNI152_T1_1mm.nii.gz │ │ ├── anatomical.nii │ │ ├── example_nifti2.nii.gz │ │ ├── test_input.txt │ │ └── wrong_format.txt │ ├── errors_test.py │ ├── inputs_test.py │ └── transcriptomics_test.py └── transcriptomics.py ├── pytest.ini ├── requirements.txt └── setup.py /.coveragerc: -------------------------------------------------------------------------------- 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