├── .github └── workflows │ ├── binder_badge.yml │ └── repo2docker.yml ├── .gitignore ├── CalculateSharpness.ipynb ├── Compound.ipynb ├── Dockerfile ├── Figure_1_Sampling_of_Phenotypes.ipynb ├── GeneNetwork.ipynb ├── GenesToPhenotypes.ipynb ├── Getting_Started.ipynb ├── HPA.ipynb ├── IDR_API_example_script.ipynb ├── LICENSE.txt ├── PCAanalysisOfCharmFeatures.ipynb ├── QueryIDRWithGeneLists.ipynb ├── README.ipynb ├── README.md ├── RohnPhenotypeClustering.ipynb ├── SysgroOverview.ipynb ├── SysgroRoiLength.ipynb ├── Using_Jupyter.ipynb ├── binder ├── environment.yml └── postBuild ├── docker ├── environment-python3-idr.yml ├── logo-32x32.png ├── logo-64x64.png ├── test.sh └── test_notebooks.sh ├── humanmine.ipynb ├── images └── compound_figure.png ├── includes ├── CMPOAccessionToPhenotypeCategories.csv ├── CMPOAccessionToPhenotypeCategoriesNov2016.csv ├── FiveExampleGenes.txt ├── HeatmapToFigure.jpg ├── HumanMineIDR.png ├── PlateToHeatmap.jpg ├── TableOfGenesWithElongatedCellPhenotype.csv ├── figure1_rohn_phenotype_clustering.png ├── login_1.png ├── login_2.png ├── romero_overview_2.png └── screenshot_01.png └── solutions └── GenesToPhenotypesSolutions.ipynb /.github/workflows/binder_badge.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IDR/idr-notebooks/HEAD/.github/workflows/binder_badge.yml -------------------------------------------------------------------------------- /.github/workflows/repo2docker.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IDR/idr-notebooks/HEAD/.github/workflows/repo2docker.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IDR/idr-notebooks/HEAD/.gitignore -------------------------------------------------------------------------------- /CalculateSharpness.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IDR/idr-notebooks/HEAD/CalculateSharpness.ipynb -------------------------------------------------------------------------------- /Compound.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IDR/idr-notebooks/HEAD/Compound.ipynb -------------------------------------------------------------------------------- /Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IDR/idr-notebooks/HEAD/Dockerfile -------------------------------------------------------------------------------- /Figure_1_Sampling_of_Phenotypes.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IDR/idr-notebooks/HEAD/Figure_1_Sampling_of_Phenotypes.ipynb -------------------------------------------------------------------------------- /GeneNetwork.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IDR/idr-notebooks/HEAD/GeneNetwork.ipynb -------------------------------------------------------------------------------- /GenesToPhenotypes.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IDR/idr-notebooks/HEAD/GenesToPhenotypes.ipynb -------------------------------------------------------------------------------- /Getting_Started.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IDR/idr-notebooks/HEAD/Getting_Started.ipynb -------------------------------------------------------------------------------- /HPA.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IDR/idr-notebooks/HEAD/HPA.ipynb -------------------------------------------------------------------------------- /IDR_API_example_script.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IDR/idr-notebooks/HEAD/IDR_API_example_script.ipynb -------------------------------------------------------------------------------- /LICENSE.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IDR/idr-notebooks/HEAD/LICENSE.txt -------------------------------------------------------------------------------- /PCAanalysisOfCharmFeatures.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IDR/idr-notebooks/HEAD/PCAanalysisOfCharmFeatures.ipynb -------------------------------------------------------------------------------- /QueryIDRWithGeneLists.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IDR/idr-notebooks/HEAD/QueryIDRWithGeneLists.ipynb -------------------------------------------------------------------------------- /README.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IDR/idr-notebooks/HEAD/README.ipynb -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IDR/idr-notebooks/HEAD/README.md -------------------------------------------------------------------------------- /RohnPhenotypeClustering.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IDR/idr-notebooks/HEAD/RohnPhenotypeClustering.ipynb -------------------------------------------------------------------------------- /SysgroOverview.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IDR/idr-notebooks/HEAD/SysgroOverview.ipynb -------------------------------------------------------------------------------- /SysgroRoiLength.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IDR/idr-notebooks/HEAD/SysgroRoiLength.ipynb -------------------------------------------------------------------------------- /Using_Jupyter.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IDR/idr-notebooks/HEAD/Using_Jupyter.ipynb -------------------------------------------------------------------------------- /binder/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IDR/idr-notebooks/HEAD/binder/environment.yml -------------------------------------------------------------------------------- /binder/postBuild: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IDR/idr-notebooks/HEAD/binder/postBuild -------------------------------------------------------------------------------- /docker/environment-python3-idr.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IDR/idr-notebooks/HEAD/docker/environment-python3-idr.yml -------------------------------------------------------------------------------- /docker/logo-32x32.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IDR/idr-notebooks/HEAD/docker/logo-32x32.png -------------------------------------------------------------------------------- /docker/logo-64x64.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IDR/idr-notebooks/HEAD/docker/logo-64x64.png -------------------------------------------------------------------------------- /docker/test.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IDR/idr-notebooks/HEAD/docker/test.sh -------------------------------------------------------------------------------- /docker/test_notebooks.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IDR/idr-notebooks/HEAD/docker/test_notebooks.sh -------------------------------------------------------------------------------- /humanmine.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IDR/idr-notebooks/HEAD/humanmine.ipynb -------------------------------------------------------------------------------- /images/compound_figure.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IDR/idr-notebooks/HEAD/images/compound_figure.png -------------------------------------------------------------------------------- /includes/CMPOAccessionToPhenotypeCategories.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IDR/idr-notebooks/HEAD/includes/CMPOAccessionToPhenotypeCategories.csv -------------------------------------------------------------------------------- /includes/CMPOAccessionToPhenotypeCategoriesNov2016.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IDR/idr-notebooks/HEAD/includes/CMPOAccessionToPhenotypeCategoriesNov2016.csv -------------------------------------------------------------------------------- /includes/FiveExampleGenes.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IDR/idr-notebooks/HEAD/includes/FiveExampleGenes.txt -------------------------------------------------------------------------------- /includes/HeatmapToFigure.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IDR/idr-notebooks/HEAD/includes/HeatmapToFigure.jpg -------------------------------------------------------------------------------- /includes/HumanMineIDR.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IDR/idr-notebooks/HEAD/includes/HumanMineIDR.png -------------------------------------------------------------------------------- /includes/PlateToHeatmap.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IDR/idr-notebooks/HEAD/includes/PlateToHeatmap.jpg -------------------------------------------------------------------------------- /includes/TableOfGenesWithElongatedCellPhenotype.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IDR/idr-notebooks/HEAD/includes/TableOfGenesWithElongatedCellPhenotype.csv -------------------------------------------------------------------------------- /includes/figure1_rohn_phenotype_clustering.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IDR/idr-notebooks/HEAD/includes/figure1_rohn_phenotype_clustering.png -------------------------------------------------------------------------------- /includes/login_1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IDR/idr-notebooks/HEAD/includes/login_1.png -------------------------------------------------------------------------------- /includes/login_2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IDR/idr-notebooks/HEAD/includes/login_2.png -------------------------------------------------------------------------------- /includes/romero_overview_2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IDR/idr-notebooks/HEAD/includes/romero_overview_2.png -------------------------------------------------------------------------------- /includes/screenshot_01.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IDR/idr-notebooks/HEAD/includes/screenshot_01.png -------------------------------------------------------------------------------- /solutions/GenesToPhenotypesSolutions.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IDR/idr-notebooks/HEAD/solutions/GenesToPhenotypesSolutions.ipynb --------------------------------------------------------------------------------