├── .gitignore ├── README.md ├── assets ├── README-06dc6.png ├── README-29d38.png ├── README-353ee.png ├── README-3f6ab.png ├── README-444f2.png ├── README-46c85.png ├── README-4744f.png ├── README-4b8a6.png ├── README-4ec6c.png ├── README-4f629.png ├── README-5ca16.png ├── README-5cce1.png ├── README-5e2c0.png ├── README-65945.png ├── README-70440.png ├── README-71265.png ├── README-730d9.png ├── README-850ef.png ├── README-85460.png ├── README-96339.png ├── README-9a90a.png ├── README-a3608.png ├── README-a7dc3.png ├── README-b4b49.png ├── README-be402.png ├── README-c231a.png ├── README-c2790.png ├── README-c5811.png ├── README-c9577.png ├── README-cb4ba.png ├── README-ce808.png ├── README-d7909.png ├── README-e07a9.png ├── README-e1c29.png ├── README-e5cab.png ├── README-e71aa.png ├── README-f0915.png ├── README-f9c0c.png ├── Tutorial_install_R_packages-00e09.png ├── Tutorial_install_R_packages-18190.png ├── Tutorial_install_R_packages-8fc96.png ├── Tutorial_install_R_packages-ac2f9.png ├── Tutorial_install_R_packages-c8c58.png ├── tutorial_00_prepare_environment-109e3.png ├── tutorial_00_prepare_environment-1f498.png ├── tutorial_00_prepare_environment-436c2.png ├── tutorial_00_prepare_environment-4c1ef.png ├── tutorial_00_prepare_environment-5f577.png ├── tutorial_00_prepare_environment-646f1.png ├── tutorial_00_prepare_environment-71f59.png ├── tutorial_00_prepare_environment-b32a0.png ├── tutorial_00_prepare_environment-b4df0.png ├── tutorial_00_prepare_environment-bc64f.png ├── tutorial_01_run_jupyter_notebook-34f81.png ├── tutorial_01_run_jupyter_notebook-42197.png └── tutorial_01_run_jupyter_notebook-f5ebd.png ├── tutorial.md ├── tutorial ├── data │ ├── CCCExplorer │ │ ├── AMPK signaling pathway.txt │ │ ├── CCCExplorer.R │ │ ├── CD11CB_output │ │ │ ├── gene_exp.diff │ │ │ ├── index.html │ │ │ ├── index.html?C=D;O=A │ │ │ ├── index.html?C=D;O=D │ │ │ ├── index.html?C=M;O=A │ │ │ ├── index.html?C=M;O=D │ │ │ ├── index.html?C=N;O=A │ │ │ ├── index.html?C=N;O=D │ │ │ ├── index.html?C=S;O=A │ │ │ └── index.html?C=S;O=D │ │ ├── EP_output │ │ │ ├── gene_exp.diff │ │ │ ├── genes.read_group_tracking │ │ │ ├── index.html │ │ │ ├── index.html?C=D;O=A │ │ │ ├── index.html?C=D;O=D │ │ │ ├── index.html?C=M;O=A │ │ │ ├── index.html?C=M;O=D │ │ │ ├── index.html?C=N;O=A │ │ │ ├── index.html?C=N;O=D │ │ │ ├── index.html?C=S;O=A │ │ │ └── index.html?C=S;O=D │ │ ├── FoxO signaling pathway.txt │ │ ├── HOM_MouseHumanSequence.rpt │ │ ├── KEGG_edge_directed.txt │ │ ├── KEGG_selected_pathway.txt │ │ ├── LR_manual_revised.txt │ │ ├── MMC_output │ │ │ ├── gene_exp.diff │ │ │ ├── index.html │ │ │ ├── index.html?C=D;O=A │ │ │ ├── index.html?C=D;O=D │ │ │ ├── index.html?C=M;O=A │ │ │ ├── index.html?C=M;O=D │ │ │ ├── index.html?C=N;O=A │ │ │ ├── index.html?C=N;O=D │ │ │ ├── index.html?C=S;O=A │ │ │ └── index.html?C=S;O=D │ │ ├── Neu_output │ │ │ ├── gene_exp.diff │ │ │ ├── index.html │ │ │ ├── index.html?C=D;O=A │ │ │ ├── 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