├── .dockerignore ├── .gitignore ├── LICENSE.md ├── PageRank.py ├── PathLinker.py ├── README.md ├── __init__.py ├── data ├── 2015pathlinker-weighted.txt ├── TGF_beta │ ├── TGF_beta_Receptor-nodes.txt │ ├── TGF_beta_Receptor-nodetypes.txt │ ├── TGF_beta_Receptor-nodetypes_ss-st.txt │ ├── TGF_beta_sources.txt │ ├── TGF_beta_targets.txt │ └── test-files │ │ ├── TGF_beta-weighted-NLT-paths-comparison.py │ │ ├── TGF_beta-weighted-NLT-paths-cytoscape.txt │ │ ├── TGF_beta-weighted-NLT-paths-pathlinker.txt │ │ ├── TGF_beta-weighted-paths-comparison.py │ │ ├── TGF_beta-weighted-paths-cytoscape.txt │ │ ├── TGF_beta-weighted-paths-pathlinker.txt │ │ ├── TGF_beta_1000-paths-comparison.py │ │ ├── TGF_beta_1000-paths-cytoscape.txt │ │ └── TGF_beta_1000-paths-pathlinker.txt ├── TNFalpha │ ├── TNFalpha-nodes.txt │ ├── TNFalpha-nodetypes.txt │ ├── TNFalpha-sources.txt │ ├── TNFalpha-targets.txt │ ├── cytoscape.txt │ ├── pathlinker.txt │ └── test-files │ │ ├── TNFalpha-NLT-weighted-paths-comparison.py │ │ ├── TNFalpha-NLT-weighted-paths-cytoscape.txt │ │ ├── TNFalpha-NLT-weighted-paths-pathlinker.txt │ │ ├── TNFalpha-paths-comparison.py │ │ ├── TNFalpha-paths-cytoscape.txt │ │ ├── TNFalpha-paths-pathlinker.txt │ │ ├── TNFalpha-weighted-paths-comparison.py │ │ ├── TNFalpha-weighted-paths-cytoscape.txt │ │ └── TNFalpha-weighted-paths-pathlinker.txt └── Wnt │ ├── Wnt-pathlinker-net.txt │ ├── Wnt-pathlinker-nodetypes.txt │ ├── Wnt-sources.txt │ ├── Wnt-targets.txt │ ├── test-files │ ├── Wnt-NLT-weighted-paths-comparison.py │ ├── Wnt-NLT-weighted-paths-cytoscape.txt │ ├── Wnt-NLT-weighted-paths-pathlinker.txt │ ├── Wnt-paths-comparison.py │ ├── Wnt-paths-cytoscape.txt │ ├── Wnt-paths-pathlinker.txt │ ├── Wnt-weighted-paths-comparison.py │ ├── Wnt-weighted-paths-cytoscape.txt │ ├── Wnt-weighted-paths-pathlinker.txt │ └── benchmark.template │ └── uniqueWnt-pathlinker-net.txt ├── docker ├── Dockerfile ├── README.md └── minimal_env.yml ├── example ├── README.md ├── sample-in-net-noweights.txt ├── sample-in-net.txt ├── sample-in-nodetypes.txt ├── sample-in-teleprobs.txt ├── sample-out-paths.txt └── sample-out-ranked-edges.txt ├── ksp_Astar.py ├── parse.py ├── pathway.jpg ├── requirements.txt ├── run.py └── tests ├── __init__.py ├── test_PathLinker.py ├── test_ksp_Astar.py └── test_parse.py /.dockerignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/.dockerignore -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | *.pyc 2 | *.swp 3 | venv/ 4 | -------------------------------------------------------------------------------- /LICENSE.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/LICENSE.md -------------------------------------------------------------------------------- /PageRank.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/PageRank.py -------------------------------------------------------------------------------- /PathLinker.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/PathLinker.py -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/README.md -------------------------------------------------------------------------------- /__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /data/2015pathlinker-weighted.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/data/2015pathlinker-weighted.txt -------------------------------------------------------------------------------- /data/TGF_beta/TGF_beta_Receptor-nodes.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/data/TGF_beta/TGF_beta_Receptor-nodes.txt -------------------------------------------------------------------------------- /data/TGF_beta/TGF_beta_Receptor-nodetypes.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/data/TGF_beta/TGF_beta_Receptor-nodetypes.txt -------------------------------------------------------------------------------- /data/TGF_beta/TGF_beta_Receptor-nodetypes_ss-st.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/data/TGF_beta/TGF_beta_Receptor-nodetypes_ss-st.txt -------------------------------------------------------------------------------- /data/TGF_beta/TGF_beta_sources.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/data/TGF_beta/TGF_beta_sources.txt -------------------------------------------------------------------------------- /data/TGF_beta/TGF_beta_targets.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/data/TGF_beta/TGF_beta_targets.txt -------------------------------------------------------------------------------- /data/TGF_beta/test-files/TGF_beta-weighted-NLT-paths-comparison.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/data/TGF_beta/test-files/TGF_beta-weighted-NLT-paths-comparison.py -------------------------------------------------------------------------------- /data/TGF_beta/test-files/TGF_beta-weighted-NLT-paths-cytoscape.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/data/TGF_beta/test-files/TGF_beta-weighted-NLT-paths-cytoscape.txt -------------------------------------------------------------------------------- /data/TGF_beta/test-files/TGF_beta-weighted-NLT-paths-pathlinker.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/data/TGF_beta/test-files/TGF_beta-weighted-NLT-paths-pathlinker.txt -------------------------------------------------------------------------------- /data/TGF_beta/test-files/TGF_beta-weighted-paths-comparison.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/data/TGF_beta/test-files/TGF_beta-weighted-paths-comparison.py -------------------------------------------------------------------------------- /data/TGF_beta/test-files/TGF_beta-weighted-paths-cytoscape.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/data/TGF_beta/test-files/TGF_beta-weighted-paths-cytoscape.txt -------------------------------------------------------------------------------- /data/TGF_beta/test-files/TGF_beta-weighted-paths-pathlinker.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/data/TGF_beta/test-files/TGF_beta-weighted-paths-pathlinker.txt -------------------------------------------------------------------------------- /data/TGF_beta/test-files/TGF_beta_1000-paths-comparison.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/data/TGF_beta/test-files/TGF_beta_1000-paths-comparison.py -------------------------------------------------------------------------------- /data/TGF_beta/test-files/TGF_beta_1000-paths-cytoscape.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/data/TGF_beta/test-files/TGF_beta_1000-paths-cytoscape.txt -------------------------------------------------------------------------------- /data/TGF_beta/test-files/TGF_beta_1000-paths-pathlinker.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/data/TGF_beta/test-files/TGF_beta_1000-paths-pathlinker.txt -------------------------------------------------------------------------------- /data/TNFalpha/TNFalpha-nodes.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/data/TNFalpha/TNFalpha-nodes.txt -------------------------------------------------------------------------------- /data/TNFalpha/TNFalpha-nodetypes.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/data/TNFalpha/TNFalpha-nodetypes.txt -------------------------------------------------------------------------------- /data/TNFalpha/TNFalpha-sources.txt: -------------------------------------------------------------------------------- 1 | Q9Y6Q6 P20333 P28908 Q8IV45 -------------------------------------------------------------------------------- /data/TNFalpha/TNFalpha-targets.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/data/TNFalpha/TNFalpha-targets.txt -------------------------------------------------------------------------------- /data/TNFalpha/cytoscape.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/data/TNFalpha/cytoscape.txt -------------------------------------------------------------------------------- /data/TNFalpha/pathlinker.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/data/TNFalpha/pathlinker.txt -------------------------------------------------------------------------------- /data/TNFalpha/test-files/TNFalpha-NLT-weighted-paths-comparison.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/data/TNFalpha/test-files/TNFalpha-NLT-weighted-paths-comparison.py -------------------------------------------------------------------------------- /data/TNFalpha/test-files/TNFalpha-NLT-weighted-paths-cytoscape.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/data/TNFalpha/test-files/TNFalpha-NLT-weighted-paths-cytoscape.txt -------------------------------------------------------------------------------- /data/TNFalpha/test-files/TNFalpha-NLT-weighted-paths-pathlinker.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/data/TNFalpha/test-files/TNFalpha-NLT-weighted-paths-pathlinker.txt -------------------------------------------------------------------------------- /data/TNFalpha/test-files/TNFalpha-paths-comparison.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/data/TNFalpha/test-files/TNFalpha-paths-comparison.py -------------------------------------------------------------------------------- /data/TNFalpha/test-files/TNFalpha-paths-cytoscape.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/data/TNFalpha/test-files/TNFalpha-paths-cytoscape.txt -------------------------------------------------------------------------------- /data/TNFalpha/test-files/TNFalpha-paths-pathlinker.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/data/TNFalpha/test-files/TNFalpha-paths-pathlinker.txt -------------------------------------------------------------------------------- /data/TNFalpha/test-files/TNFalpha-weighted-paths-comparison.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/data/TNFalpha/test-files/TNFalpha-weighted-paths-comparison.py -------------------------------------------------------------------------------- /data/TNFalpha/test-files/TNFalpha-weighted-paths-cytoscape.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/data/TNFalpha/test-files/TNFalpha-weighted-paths-cytoscape.txt -------------------------------------------------------------------------------- /data/TNFalpha/test-files/TNFalpha-weighted-paths-pathlinker.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/data/TNFalpha/test-files/TNFalpha-weighted-paths-pathlinker.txt -------------------------------------------------------------------------------- /data/Wnt/Wnt-pathlinker-net.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/data/Wnt/Wnt-pathlinker-net.txt -------------------------------------------------------------------------------- /data/Wnt/Wnt-pathlinker-nodetypes.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/data/Wnt/Wnt-pathlinker-nodetypes.txt -------------------------------------------------------------------------------- /data/Wnt/Wnt-sources.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/data/Wnt/Wnt-sources.txt -------------------------------------------------------------------------------- /data/Wnt/Wnt-targets.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/data/Wnt/Wnt-targets.txt -------------------------------------------------------------------------------- /data/Wnt/test-files/Wnt-NLT-weighted-paths-comparison.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/data/Wnt/test-files/Wnt-NLT-weighted-paths-comparison.py -------------------------------------------------------------------------------- /data/Wnt/test-files/Wnt-NLT-weighted-paths-cytoscape.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/data/Wnt/test-files/Wnt-NLT-weighted-paths-cytoscape.txt -------------------------------------------------------------------------------- /data/Wnt/test-files/Wnt-NLT-weighted-paths-pathlinker.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/data/Wnt/test-files/Wnt-NLT-weighted-paths-pathlinker.txt -------------------------------------------------------------------------------- /data/Wnt/test-files/Wnt-paths-comparison.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/data/Wnt/test-files/Wnt-paths-comparison.py -------------------------------------------------------------------------------- /data/Wnt/test-files/Wnt-paths-cytoscape.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/data/Wnt/test-files/Wnt-paths-cytoscape.txt -------------------------------------------------------------------------------- /data/Wnt/test-files/Wnt-paths-pathlinker.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/data/Wnt/test-files/Wnt-paths-pathlinker.txt -------------------------------------------------------------------------------- /data/Wnt/test-files/Wnt-weighted-paths-comparison.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/data/Wnt/test-files/Wnt-weighted-paths-comparison.py -------------------------------------------------------------------------------- /data/Wnt/test-files/Wnt-weighted-paths-cytoscape.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/data/Wnt/test-files/Wnt-weighted-paths-cytoscape.txt -------------------------------------------------------------------------------- /data/Wnt/test-files/Wnt-weighted-paths-pathlinker.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/data/Wnt/test-files/Wnt-weighted-paths-pathlinker.txt -------------------------------------------------------------------------------- /data/Wnt/test-files/benchmark.template: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/data/Wnt/test-files/benchmark.template -------------------------------------------------------------------------------- /data/Wnt/uniqueWnt-pathlinker-net.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/data/Wnt/uniqueWnt-pathlinker-net.txt -------------------------------------------------------------------------------- /docker/Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/docker/Dockerfile -------------------------------------------------------------------------------- /docker/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/docker/README.md -------------------------------------------------------------------------------- /docker/minimal_env.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/docker/minimal_env.yml -------------------------------------------------------------------------------- /example/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/example/README.md -------------------------------------------------------------------------------- /example/sample-in-net-noweights.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/example/sample-in-net-noweights.txt -------------------------------------------------------------------------------- /example/sample-in-net.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/example/sample-in-net.txt -------------------------------------------------------------------------------- /example/sample-in-nodetypes.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/example/sample-in-nodetypes.txt -------------------------------------------------------------------------------- /example/sample-in-teleprobs.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/example/sample-in-teleprobs.txt -------------------------------------------------------------------------------- /example/sample-out-paths.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/example/sample-out-paths.txt -------------------------------------------------------------------------------- /example/sample-out-ranked-edges.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/example/sample-out-ranked-edges.txt -------------------------------------------------------------------------------- /ksp_Astar.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/ksp_Astar.py -------------------------------------------------------------------------------- /parse.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/parse.py -------------------------------------------------------------------------------- /pathway.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/pathway.jpg -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- 1 | decorator==4.1.2 2 | networkx==1.11 3 | pkg-resources==0.0.0 4 | -------------------------------------------------------------------------------- /run.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/run.py -------------------------------------------------------------------------------- /tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/test_PathLinker.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/tests/test_PathLinker.py -------------------------------------------------------------------------------- /tests/test_ksp_Astar.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/tests/test_ksp_Astar.py -------------------------------------------------------------------------------- /tests/test_parse.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/PathLinker/HEAD/tests/test_parse.py --------------------------------------------------------------------------------