├── CliXO_MuSIC.zip ├── Examples ├── .ipynb_checkpoints │ └── Step-by-step guide to build MuSIC v1-checkpoint.ipynb ├── APMS_embedding.MuSIC.csv ├── HumanCellMap_edge_matrix.csv ├── IF_image_embedding.csv ├── MuSIC_avgPred_ytrue.csv ├── MuSIC_predicted_proximity.txt ├── MuSIC_proteins.txt └── toy │ ├── toy_APMS_embedding.csv │ ├── toy_IF_image_embedding.csv │ └── toy_proteins.txt ├── Figures ├── GitHub_CommunityDetection_update.png ├── GitHub_RandomForest.png ├── GitHub_calibration.png └── GitHub_overview.png ├── LICENSE.txt ├── README.md ├── Step-by-step guide to build MuSIC v1.ipynb ├── calibrate_pairwise_distance.py ├── community_detection.py ├── community_detection ├── cap_louvain.py ├── clean_up.py ├── louvain_partition.py ├── mature_hier_structure.py ├── predict_size.py ├── process_clixoOutFile.py └── trim_clixo.py ├── data ├── GO_CC_human_no_hpa.txt ├── GO_annotated_proteins.txt └── calibration.txt ├── example_buid_music_v1.sh ├── hierarchy_evaluation.py ├── installation ├── install.sh └── requirements.txt ├── music_utils.py ├── random_forest ├── __pycache__ │ ├── balance_sample.cpython-36.pyc │ ├── format_emd.cpython-36.pyc │ └── format_emd_data.cpython-36.pyc ├── balance_sample.py └── format_emd_data.py ├── random_forest_output.py ├── random_forest_samples.py ├── run_random_forest.py └── toy_example.sh /CliXO_MuSIC.zip: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idekerlab/MuSIC/HEAD/CliXO_MuSIC.zip -------------------------------------------------------------------------------- /Examples/.ipynb_checkpoints/Step-by-step guide to build MuSIC v1-checkpoint.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idekerlab/MuSIC/HEAD/Examples/.ipynb_checkpoints/Step-by-step guide to build MuSIC v1-checkpoint.ipynb -------------------------------------------------------------------------------- /Examples/APMS_embedding.MuSIC.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idekerlab/MuSIC/HEAD/Examples/APMS_embedding.MuSIC.csv -------------------------------------------------------------------------------- /Examples/HumanCellMap_edge_matrix.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idekerlab/MuSIC/HEAD/Examples/HumanCellMap_edge_matrix.csv -------------------------------------------------------------------------------- /Examples/IF_image_embedding.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idekerlab/MuSIC/HEAD/Examples/IF_image_embedding.csv -------------------------------------------------------------------------------- /Examples/MuSIC_avgPred_ytrue.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idekerlab/MuSIC/HEAD/Examples/MuSIC_avgPred_ytrue.csv -------------------------------------------------------------------------------- /Examples/MuSIC_predicted_proximity.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idekerlab/MuSIC/HEAD/Examples/MuSIC_predicted_proximity.txt -------------------------------------------------------------------------------- /Examples/MuSIC_proteins.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idekerlab/MuSIC/HEAD/Examples/MuSIC_proteins.txt -------------------------------------------------------------------------------- /Examples/toy/toy_APMS_embedding.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idekerlab/MuSIC/HEAD/Examples/toy/toy_APMS_embedding.csv -------------------------------------------------------------------------------- /Examples/toy/toy_IF_image_embedding.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idekerlab/MuSIC/HEAD/Examples/toy/toy_IF_image_embedding.csv -------------------------------------------------------------------------------- /Examples/toy/toy_proteins.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idekerlab/MuSIC/HEAD/Examples/toy/toy_proteins.txt -------------------------------------------------------------------------------- /Figures/GitHub_CommunityDetection_update.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idekerlab/MuSIC/HEAD/Figures/GitHub_CommunityDetection_update.png -------------------------------------------------------------------------------- /Figures/GitHub_RandomForest.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idekerlab/MuSIC/HEAD/Figures/GitHub_RandomForest.png -------------------------------------------------------------------------------- /Figures/GitHub_calibration.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idekerlab/MuSIC/HEAD/Figures/GitHub_calibration.png -------------------------------------------------------------------------------- /Figures/GitHub_overview.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idekerlab/MuSIC/HEAD/Figures/GitHub_overview.png -------------------------------------------------------------------------------- /LICENSE.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idekerlab/MuSIC/HEAD/LICENSE.txt -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idekerlab/MuSIC/HEAD/README.md -------------------------------------------------------------------------------- /Step-by-step guide to build MuSIC v1.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idekerlab/MuSIC/HEAD/Step-by-step guide to build MuSIC v1.ipynb -------------------------------------------------------------------------------- /calibrate_pairwise_distance.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idekerlab/MuSIC/HEAD/calibrate_pairwise_distance.py -------------------------------------------------------------------------------- /community_detection.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idekerlab/MuSIC/HEAD/community_detection.py -------------------------------------------------------------------------------- /community_detection/cap_louvain.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idekerlab/MuSIC/HEAD/community_detection/cap_louvain.py -------------------------------------------------------------------------------- /community_detection/clean_up.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idekerlab/MuSIC/HEAD/community_detection/clean_up.py -------------------------------------------------------------------------------- /community_detection/louvain_partition.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idekerlab/MuSIC/HEAD/community_detection/louvain_partition.py -------------------------------------------------------------------------------- /community_detection/mature_hier_structure.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idekerlab/MuSIC/HEAD/community_detection/mature_hier_structure.py -------------------------------------------------------------------------------- /community_detection/predict_size.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idekerlab/MuSIC/HEAD/community_detection/predict_size.py -------------------------------------------------------------------------------- /community_detection/process_clixoOutFile.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idekerlab/MuSIC/HEAD/community_detection/process_clixoOutFile.py -------------------------------------------------------------------------------- /community_detection/trim_clixo.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idekerlab/MuSIC/HEAD/community_detection/trim_clixo.py -------------------------------------------------------------------------------- /data/GO_CC_human_no_hpa.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idekerlab/MuSIC/HEAD/data/GO_CC_human_no_hpa.txt -------------------------------------------------------------------------------- /data/GO_annotated_proteins.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idekerlab/MuSIC/HEAD/data/GO_annotated_proteins.txt -------------------------------------------------------------------------------- /data/calibration.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idekerlab/MuSIC/HEAD/data/calibration.txt -------------------------------------------------------------------------------- /example_buid_music_v1.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idekerlab/MuSIC/HEAD/example_buid_music_v1.sh -------------------------------------------------------------------------------- /hierarchy_evaluation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idekerlab/MuSIC/HEAD/hierarchy_evaluation.py -------------------------------------------------------------------------------- /installation/install.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idekerlab/MuSIC/HEAD/installation/install.sh -------------------------------------------------------------------------------- /installation/requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idekerlab/MuSIC/HEAD/installation/requirements.txt -------------------------------------------------------------------------------- /music_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idekerlab/MuSIC/HEAD/music_utils.py -------------------------------------------------------------------------------- /random_forest/__pycache__/balance_sample.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idekerlab/MuSIC/HEAD/random_forest/__pycache__/balance_sample.cpython-36.pyc -------------------------------------------------------------------------------- /random_forest/__pycache__/format_emd.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idekerlab/MuSIC/HEAD/random_forest/__pycache__/format_emd.cpython-36.pyc -------------------------------------------------------------------------------- /random_forest/__pycache__/format_emd_data.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idekerlab/MuSIC/HEAD/random_forest/__pycache__/format_emd_data.cpython-36.pyc -------------------------------------------------------------------------------- /random_forest/balance_sample.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idekerlab/MuSIC/HEAD/random_forest/balance_sample.py -------------------------------------------------------------------------------- /random_forest/format_emd_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idekerlab/MuSIC/HEAD/random_forest/format_emd_data.py -------------------------------------------------------------------------------- /random_forest_output.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idekerlab/MuSIC/HEAD/random_forest_output.py -------------------------------------------------------------------------------- /random_forest_samples.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idekerlab/MuSIC/HEAD/random_forest_samples.py -------------------------------------------------------------------------------- /run_random_forest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idekerlab/MuSIC/HEAD/run_random_forest.py -------------------------------------------------------------------------------- /toy_example.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idekerlab/MuSIC/HEAD/toy_example.sh --------------------------------------------------------------------------------