├── .gitignore ├── BoolODE ├── __init__.py ├── model_generator.py ├── parameters.yaml ├── post_processing.py ├── run_experiment.py ├── simulator.py └── utils.py ├── LICENSE ├── README.md ├── boolode.py ├── config-files ├── beeline-inputs-boolean.yaml ├── beeline-inputs-synthetic.yaml ├── config.yaml └── example-config.yaml ├── data ├── EMT.txt ├── GSD.txt ├── GSD_ics.txt ├── HSC.txt ├── HSC_ics.txt ├── VSC.txt ├── dyn-bifurcating-converging.txt ├── dyn-bifurcating-converging_ics.txt ├── dyn-bifurcating-converging_strengths.txt ├── dyn-bifurcating-loop.txt ├── dyn-bifurcating-loop_ics.txt ├── dyn-bifurcating-loop_strengths.txt ├── dyn-bifurcating.txt ├── dyn-bifurcating_ics.txt ├── dyn-bifurcating_strengths.txt ├── dyn-consecutive-bifurcating-inputs.txt ├── dyn-consecutive-bifurcating.txt ├── dyn-consecutive-bifurcating_ics.txt ├── dyn-consecutive-bifurcating_strengths.txt ├── dyn-converging.txt ├── dyn-converging_ics.txt ├── dyn-cycle.txt ├── dyn-cycle_ics.txt ├── dyn-cycle_strengths.txt ├── dyn-linear-long.txt ├── dyn-linear-long_ics.txt ├── dyn-linear-long_strengths.txt ├── dyn-linear.txt ├── dyn-linear_ics.txt ├── dyn-linear_strengths.txt ├── dyn-trifurcating.txt ├── dyn-trifurcating_ics.txt ├── dyn-trifurcating_strengths.txt ├── mCAD.txt ├── mCAD_ics.txt ├── mutual-inhibition.txt ├── randBool.txt ├── randNet.txt └── test_vars.txt ├── requirements.txt ├── scripts ├── genDropouts.py ├── genSamples.py ├── genVis.py ├── runSlingshot.py └── script-to-generate-datasets.sh ├── silhouetteanalysis.py └── slingshot-docker ├── Dockerfile ├── README.md └── run_slingshot.R /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/.gitignore -------------------------------------------------------------------------------- /BoolODE/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/BoolODE/__init__.py -------------------------------------------------------------------------------- /BoolODE/model_generator.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/BoolODE/model_generator.py -------------------------------------------------------------------------------- /BoolODE/parameters.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/BoolODE/parameters.yaml -------------------------------------------------------------------------------- /BoolODE/post_processing.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/BoolODE/post_processing.py -------------------------------------------------------------------------------- /BoolODE/run_experiment.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/BoolODE/run_experiment.py -------------------------------------------------------------------------------- /BoolODE/simulator.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/BoolODE/simulator.py -------------------------------------------------------------------------------- /BoolODE/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/BoolODE/utils.py -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/README.md -------------------------------------------------------------------------------- /boolode.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/boolode.py -------------------------------------------------------------------------------- /config-files/beeline-inputs-boolean.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/config-files/beeline-inputs-boolean.yaml -------------------------------------------------------------------------------- /config-files/beeline-inputs-synthetic.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/config-files/beeline-inputs-synthetic.yaml -------------------------------------------------------------------------------- /config-files/config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/config-files/config.yaml -------------------------------------------------------------------------------- /config-files/example-config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/config-files/example-config.yaml -------------------------------------------------------------------------------- /data/EMT.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/data/EMT.txt -------------------------------------------------------------------------------- /data/GSD.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/data/GSD.txt -------------------------------------------------------------------------------- /data/GSD_ics.txt: -------------------------------------------------------------------------------- 1 | Genes Values 2 | ['UGR'] [2] 3 | -------------------------------------------------------------------------------- /data/HSC.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/data/HSC.txt -------------------------------------------------------------------------------- /data/HSC_ics.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/data/HSC_ics.txt -------------------------------------------------------------------------------- /data/VSC.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/data/VSC.txt -------------------------------------------------------------------------------- /data/dyn-bifurcating-converging.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/data/dyn-bifurcating-converging.txt -------------------------------------------------------------------------------- /data/dyn-bifurcating-converging_ics.txt: -------------------------------------------------------------------------------- 1 | Genes Values 2 | ['g1'] [1] 3 | -------------------------------------------------------------------------------- /data/dyn-bifurcating-converging_strengths.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/data/dyn-bifurcating-converging_strengths.txt -------------------------------------------------------------------------------- /data/dyn-bifurcating-loop.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/data/dyn-bifurcating-loop.txt -------------------------------------------------------------------------------- /data/dyn-bifurcating-loop_ics.txt: -------------------------------------------------------------------------------- 1 | Genes Values 2 | ['g1'] [1] 3 | -------------------------------------------------------------------------------- /data/dyn-bifurcating-loop_strengths.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/data/dyn-bifurcating-loop_strengths.txt -------------------------------------------------------------------------------- /data/dyn-bifurcating.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/data/dyn-bifurcating.txt -------------------------------------------------------------------------------- /data/dyn-bifurcating_ics.txt: -------------------------------------------------------------------------------- 1 | Genes Values 2 | ['g1'] [1] 3 | -------------------------------------------------------------------------------- /data/dyn-bifurcating_strengths.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/data/dyn-bifurcating_strengths.txt -------------------------------------------------------------------------------- /data/dyn-consecutive-bifurcating-inputs.txt: -------------------------------------------------------------------------------- 1 | Input Value 2 | g1 1 3 | -------------------------------------------------------------------------------- /data/dyn-consecutive-bifurcating.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/data/dyn-consecutive-bifurcating.txt -------------------------------------------------------------------------------- /data/dyn-consecutive-bifurcating_ics.txt: -------------------------------------------------------------------------------- 1 | Genes Values 2 | ['g1'] [1] 3 | -------------------------------------------------------------------------------- /data/dyn-consecutive-bifurcating_strengths.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/data/dyn-consecutive-bifurcating_strengths.txt -------------------------------------------------------------------------------- /data/dyn-converging.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/data/dyn-converging.txt -------------------------------------------------------------------------------- /data/dyn-converging_ics.txt: -------------------------------------------------------------------------------- 1 | Genes Values 2 | ['g1'] [1] 3 | -------------------------------------------------------------------------------- /data/dyn-cycle.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/data/dyn-cycle.txt -------------------------------------------------------------------------------- /data/dyn-cycle_ics.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/data/dyn-cycle_ics.txt -------------------------------------------------------------------------------- /data/dyn-cycle_strengths.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/data/dyn-cycle_strengths.txt -------------------------------------------------------------------------------- /data/dyn-linear-long.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/data/dyn-linear-long.txt -------------------------------------------------------------------------------- /data/dyn-linear-long_ics.txt: -------------------------------------------------------------------------------- 1 | Genes Values 2 | ['g1'] [1] 3 | -------------------------------------------------------------------------------- /data/dyn-linear-long_strengths.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/data/dyn-linear-long_strengths.txt -------------------------------------------------------------------------------- /data/dyn-linear.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/data/dyn-linear.txt -------------------------------------------------------------------------------- /data/dyn-linear_ics.txt: -------------------------------------------------------------------------------- 1 | Genes Values 2 | ['g1'] [1] 3 | -------------------------------------------------------------------------------- /data/dyn-linear_strengths.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/data/dyn-linear_strengths.txt -------------------------------------------------------------------------------- /data/dyn-trifurcating.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/data/dyn-trifurcating.txt -------------------------------------------------------------------------------- /data/dyn-trifurcating_ics.txt: -------------------------------------------------------------------------------- 1 | Genes Values 2 | ['g1'] [1] 3 | -------------------------------------------------------------------------------- /data/dyn-trifurcating_strengths.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/data/dyn-trifurcating_strengths.txt -------------------------------------------------------------------------------- /data/mCAD.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/data/mCAD.txt -------------------------------------------------------------------------------- /data/mCAD_ics.txt: -------------------------------------------------------------------------------- 1 | Genes Values 2 | ['Fgf8'] [2] 3 | -------------------------------------------------------------------------------- /data/mutual-inhibition.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/data/mutual-inhibition.txt -------------------------------------------------------------------------------- /data/randBool.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/data/randBool.txt -------------------------------------------------------------------------------- /data/randNet.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/data/randNet.txt -------------------------------------------------------------------------------- /data/test_vars.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/data/test_vars.txt -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/requirements.txt -------------------------------------------------------------------------------- /scripts/genDropouts.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/scripts/genDropouts.py -------------------------------------------------------------------------------- /scripts/genSamples.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/scripts/genSamples.py -------------------------------------------------------------------------------- /scripts/genVis.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/scripts/genVis.py -------------------------------------------------------------------------------- /scripts/runSlingshot.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/scripts/runSlingshot.py -------------------------------------------------------------------------------- /scripts/script-to-generate-datasets.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/scripts/script-to-generate-datasets.sh -------------------------------------------------------------------------------- /silhouetteanalysis.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/silhouetteanalysis.py -------------------------------------------------------------------------------- /slingshot-docker/Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/slingshot-docker/Dockerfile -------------------------------------------------------------------------------- /slingshot-docker/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/slingshot-docker/README.md -------------------------------------------------------------------------------- /slingshot-docker/run_slingshot.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Murali-group/BoolODE/HEAD/slingshot-docker/run_slingshot.R --------------------------------------------------------------------------------