├── .gitignore ├── .travis.yml ├── CHANGELOG.rst ├── CHANGELOG_old.rst ├── LICENSE ├── MANIFEST.in ├── README.rst ├── docs ├── Makefile ├── make.bat ├── rtd_requirements.txt ├── run_sphinx-apidoc.sh └── source │ ├── _static │ └── gopca.png │ ├── api │ ├── config.rst │ ├── gopca.rst │ ├── index.rst │ ├── params.rst │ ├── run.rst │ ├── signature.rst │ └── signature_matrix.rst │ ├── citing.rst │ ├── cli.rst │ ├── conf.py │ ├── demos.rst │ ├── gene_set_files.rst │ ├── gene_sets.rst │ ├── go_annotations.rst │ ├── go_pca.rst │ ├── index.rst │ ├── install.rst │ ├── install_mac.rst │ ├── install_ubuntu.rst │ ├── install_windows.rst │ ├── intro.rst │ ├── license.rst │ ├── notebooks │ ├── DMAP_analysis.ipynb │ └── Demo_DMAP.ipynb │ └── running.rst ├── gopca ├── __init__.py ├── cli │ ├── __init__.py │ ├── arguments.py │ ├── combine_signatures.py │ ├── convert_to_matlab.py │ ├── extract_go_gene_sets.py │ ├── extract_signature_matrix.py │ ├── extract_signatures.py │ ├── extract_signatures_excel.py │ ├── filter_signatures.py │ ├── go_pca.py │ ├── plot_signature_matrix.py │ └── print_info.py ├── config.py ├── gopca.py ├── params.py ├── run.py ├── signature.py ├── signature_matrix.py └── util.py ├── pylintrc ├── requirements.txt ├── setup.py └── tests ├── 01_fake_data ├── conftest.py ├── test_config.py ├── test_gopca.py ├── test_params.py ├── test_signature.py └── test_signature_matrix.py └── 02_real_data ├── 01_cli ├── conftest.py ├── test_extract_signature_matrix.py ├── test_extract_signatures.py ├── test_extract_signatures_excel.py ├── test_go_pca.py ├── test_plot_signature_matrix.py └── test_print_info.py ├── 02_pythonapi ├── conftest.py ├── test_real_gopca.py └── test_real_signature_matrix.py └── conftest.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/.gitignore -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/.travis.yml -------------------------------------------------------------------------------- /CHANGELOG.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/CHANGELOG.rst -------------------------------------------------------------------------------- /CHANGELOG_old.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/CHANGELOG_old.rst -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/LICENSE -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/MANIFEST.in -------------------------------------------------------------------------------- /README.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/README.rst -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/docs/Makefile -------------------------------------------------------------------------------- /docs/make.bat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/docs/make.bat -------------------------------------------------------------------------------- /docs/rtd_requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/docs/rtd_requirements.txt -------------------------------------------------------------------------------- /docs/run_sphinx-apidoc.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/docs/run_sphinx-apidoc.sh -------------------------------------------------------------------------------- /docs/source/_static/gopca.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/docs/source/_static/gopca.png -------------------------------------------------------------------------------- /docs/source/api/config.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/docs/source/api/config.rst -------------------------------------------------------------------------------- /docs/source/api/gopca.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/docs/source/api/gopca.rst -------------------------------------------------------------------------------- /docs/source/api/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/docs/source/api/index.rst -------------------------------------------------------------------------------- /docs/source/api/params.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/docs/source/api/params.rst -------------------------------------------------------------------------------- /docs/source/api/run.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/docs/source/api/run.rst -------------------------------------------------------------------------------- /docs/source/api/signature.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/docs/source/api/signature.rst -------------------------------------------------------------------------------- /docs/source/api/signature_matrix.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/docs/source/api/signature_matrix.rst -------------------------------------------------------------------------------- /docs/source/citing.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/docs/source/citing.rst -------------------------------------------------------------------------------- /docs/source/cli.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/docs/source/cli.rst -------------------------------------------------------------------------------- /docs/source/conf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/docs/source/conf.py -------------------------------------------------------------------------------- /docs/source/demos.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/docs/source/demos.rst -------------------------------------------------------------------------------- /docs/source/gene_set_files.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/docs/source/gene_set_files.rst -------------------------------------------------------------------------------- /docs/source/gene_sets.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/docs/source/gene_sets.rst -------------------------------------------------------------------------------- /docs/source/go_annotations.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/docs/source/go_annotations.rst -------------------------------------------------------------------------------- /docs/source/go_pca.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/docs/source/go_pca.rst -------------------------------------------------------------------------------- /docs/source/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/docs/source/index.rst -------------------------------------------------------------------------------- /docs/source/install.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/docs/source/install.rst -------------------------------------------------------------------------------- /docs/source/install_mac.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/docs/source/install_mac.rst -------------------------------------------------------------------------------- /docs/source/install_ubuntu.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/docs/source/install_ubuntu.rst -------------------------------------------------------------------------------- /docs/source/install_windows.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/docs/source/install_windows.rst -------------------------------------------------------------------------------- /docs/source/intro.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/docs/source/intro.rst -------------------------------------------------------------------------------- /docs/source/license.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/docs/source/license.rst -------------------------------------------------------------------------------- /docs/source/notebooks/DMAP_analysis.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/docs/source/notebooks/DMAP_analysis.ipynb -------------------------------------------------------------------------------- /docs/source/notebooks/Demo_DMAP.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/docs/source/notebooks/Demo_DMAP.ipynb -------------------------------------------------------------------------------- /docs/source/running.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/docs/source/running.rst -------------------------------------------------------------------------------- /gopca/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/gopca/__init__.py -------------------------------------------------------------------------------- /gopca/cli/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /gopca/cli/arguments.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/gopca/cli/arguments.py -------------------------------------------------------------------------------- /gopca/cli/combine_signatures.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/gopca/cli/combine_signatures.py -------------------------------------------------------------------------------- /gopca/cli/convert_to_matlab.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/gopca/cli/convert_to_matlab.py -------------------------------------------------------------------------------- /gopca/cli/extract_go_gene_sets.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/gopca/cli/extract_go_gene_sets.py -------------------------------------------------------------------------------- /gopca/cli/extract_signature_matrix.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/gopca/cli/extract_signature_matrix.py -------------------------------------------------------------------------------- /gopca/cli/extract_signatures.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/gopca/cli/extract_signatures.py -------------------------------------------------------------------------------- /gopca/cli/extract_signatures_excel.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/gopca/cli/extract_signatures_excel.py -------------------------------------------------------------------------------- /gopca/cli/filter_signatures.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/gopca/cli/filter_signatures.py -------------------------------------------------------------------------------- /gopca/cli/go_pca.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/gopca/cli/go_pca.py -------------------------------------------------------------------------------- /gopca/cli/plot_signature_matrix.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/gopca/cli/plot_signature_matrix.py -------------------------------------------------------------------------------- /gopca/cli/print_info.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/gopca/cli/print_info.py -------------------------------------------------------------------------------- /gopca/config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/gopca/config.py -------------------------------------------------------------------------------- /gopca/gopca.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/gopca/gopca.py -------------------------------------------------------------------------------- /gopca/params.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/gopca/params.py -------------------------------------------------------------------------------- /gopca/run.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/gopca/run.py -------------------------------------------------------------------------------- /gopca/signature.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/gopca/signature.py -------------------------------------------------------------------------------- /gopca/signature_matrix.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/gopca/signature_matrix.py -------------------------------------------------------------------------------- /gopca/util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/gopca/util.py -------------------------------------------------------------------------------- /pylintrc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/pylintrc -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/requirements.txt -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/setup.py -------------------------------------------------------------------------------- /tests/01_fake_data/conftest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/tests/01_fake_data/conftest.py -------------------------------------------------------------------------------- /tests/01_fake_data/test_config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/tests/01_fake_data/test_config.py -------------------------------------------------------------------------------- /tests/01_fake_data/test_gopca.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/tests/01_fake_data/test_gopca.py -------------------------------------------------------------------------------- /tests/01_fake_data/test_params.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/tests/01_fake_data/test_params.py -------------------------------------------------------------------------------- /tests/01_fake_data/test_signature.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/tests/01_fake_data/test_signature.py -------------------------------------------------------------------------------- /tests/01_fake_data/test_signature_matrix.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/tests/01_fake_data/test_signature_matrix.py -------------------------------------------------------------------------------- /tests/02_real_data/01_cli/conftest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/tests/02_real_data/01_cli/conftest.py -------------------------------------------------------------------------------- /tests/02_real_data/01_cli/test_extract_signature_matrix.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/tests/02_real_data/01_cli/test_extract_signature_matrix.py -------------------------------------------------------------------------------- /tests/02_real_data/01_cli/test_extract_signatures.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/tests/02_real_data/01_cli/test_extract_signatures.py -------------------------------------------------------------------------------- /tests/02_real_data/01_cli/test_extract_signatures_excel.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/tests/02_real_data/01_cli/test_extract_signatures_excel.py -------------------------------------------------------------------------------- /tests/02_real_data/01_cli/test_go_pca.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/tests/02_real_data/01_cli/test_go_pca.py -------------------------------------------------------------------------------- /tests/02_real_data/01_cli/test_plot_signature_matrix.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/tests/02_real_data/01_cli/test_plot_signature_matrix.py -------------------------------------------------------------------------------- /tests/02_real_data/01_cli/test_print_info.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/tests/02_real_data/01_cli/test_print_info.py -------------------------------------------------------------------------------- /tests/02_real_data/02_pythonapi/conftest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/tests/02_real_data/02_pythonapi/conftest.py -------------------------------------------------------------------------------- /tests/02_real_data/02_pythonapi/test_real_gopca.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/tests/02_real_data/02_pythonapi/test_real_gopca.py -------------------------------------------------------------------------------- /tests/02_real_data/02_pythonapi/test_real_signature_matrix.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/tests/02_real_data/02_pythonapi/test_real_signature_matrix.py -------------------------------------------------------------------------------- /tests/02_real_data/conftest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/gopca/HEAD/tests/02_real_data/conftest.py --------------------------------------------------------------------------------