├── .DS_Store ├── .gitattributes ├── .gitignore ├── LICENSE ├── README.md ├── depr ├── scripts │ ├── .gitkeep │ ├── veres-fate.sh │ ├── weinreb-fate.sh │ └── weinreb-interpolate.sh ├── veres.py └── weinreb.py ├── docs ├── .DS_Store ├── .bundle │ └── config ├── .gitignore ├── Gemfile ├── Gemfile.lock ├── _config.yml ├── _data │ ├── examples.json │ ├── navigation.yml │ └── tools.json ├── _includes │ ├── head.html │ ├── header.html │ └── navbar.html ├── _layouts │ ├── cli.html │ ├── core.html │ ├── document.html │ └── home.html ├── _site │ ├── file_formats │ │ └── index.html │ └── index.md ├── about.html ├── assets │ ├── .DS_Store │ ├── css │ │ └── styles.scss │ ├── gifs │ │ └── trajectories.gif │ └── img │ │ ├── .DS_Store │ │ ├── implementation.png │ │ └── model.png ├── documentation.html ├── file_formats.md ├── index.md ├── notebooks.html └── quickstart.html ├── notebooks ├── .gitkeep └── estimate-growth-rates.ipynb ├── prescient ├── .gitkeep ├── __init__.py ├── __main__.py ├── __pycache__ │ ├── train.cpython-37.pyc │ └── veres.cpython-37.pyc ├── commands │ ├── __init__.py │ ├── perturbation_analysis.py │ ├── process_data.py │ ├── simulate_trajectories.py │ └── train_model.py ├── perturb │ ├── __init__.py │ └── pert.py ├── simulate │ ├── __init__.py │ └── sim.py ├── train │ ├── __init__.py │ ├── model.py │ ├── run.py │ └── util.py └── utils.py ├── pyproject.toml ├── setup.cfg └── setup.py /.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/.DS_Store -------------------------------------------------------------------------------- /.gitattributes: -------------------------------------------------------------------------------- 1 | *.ipynb linguist-detectable=false 2 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/README.md -------------------------------------------------------------------------------- /depr/scripts/.gitkeep: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /depr/scripts/veres-fate.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/depr/scripts/veres-fate.sh -------------------------------------------------------------------------------- /depr/scripts/weinreb-fate.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/depr/scripts/weinreb-fate.sh -------------------------------------------------------------------------------- /depr/scripts/weinreb-interpolate.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/depr/scripts/weinreb-interpolate.sh -------------------------------------------------------------------------------- /depr/veres.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/depr/veres.py -------------------------------------------------------------------------------- /depr/weinreb.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/depr/weinreb.py -------------------------------------------------------------------------------- /docs/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/docs/.DS_Store -------------------------------------------------------------------------------- /docs/.bundle/config: -------------------------------------------------------------------------------- 1 | --- 2 | BUNDLE_PATH: "vendor/bundle" 3 | -------------------------------------------------------------------------------- /docs/.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/docs/.gitignore -------------------------------------------------------------------------------- /docs/Gemfile: -------------------------------------------------------------------------------- 1 | source 'https://rubygems.org' 2 | gem 'github-pages', "~> 214" 3 | -------------------------------------------------------------------------------- /docs/Gemfile.lock: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/docs/Gemfile.lock -------------------------------------------------------------------------------- /docs/_config.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/docs/_config.yml -------------------------------------------------------------------------------- /docs/_data/examples.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/docs/_data/examples.json -------------------------------------------------------------------------------- /docs/_data/navigation.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/docs/_data/navigation.yml -------------------------------------------------------------------------------- /docs/_data/tools.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/docs/_data/tools.json -------------------------------------------------------------------------------- /docs/_includes/head.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/docs/_includes/head.html -------------------------------------------------------------------------------- /docs/_includes/header.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/docs/_includes/header.html -------------------------------------------------------------------------------- /docs/_includes/navbar.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/docs/_includes/navbar.html -------------------------------------------------------------------------------- /docs/_layouts/cli.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/docs/_layouts/cli.html -------------------------------------------------------------------------------- /docs/_layouts/core.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/docs/_layouts/core.html -------------------------------------------------------------------------------- /docs/_layouts/document.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/docs/_layouts/document.html -------------------------------------------------------------------------------- /docs/_layouts/home.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/docs/_layouts/home.html -------------------------------------------------------------------------------- /docs/_site/file_formats/index.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/docs/_site/file_formats/index.html -------------------------------------------------------------------------------- /docs/_site/index.md: -------------------------------------------------------------------------------- 1 | # prescient 2 | -------------------------------------------------------------------------------- /docs/about.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/docs/about.html -------------------------------------------------------------------------------- /docs/assets/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/docs/assets/.DS_Store -------------------------------------------------------------------------------- /docs/assets/css/styles.scss: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/docs/assets/css/styles.scss -------------------------------------------------------------------------------- /docs/assets/gifs/trajectories.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/docs/assets/gifs/trajectories.gif -------------------------------------------------------------------------------- /docs/assets/img/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/docs/assets/img/.DS_Store -------------------------------------------------------------------------------- /docs/assets/img/implementation.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/docs/assets/img/implementation.png -------------------------------------------------------------------------------- /docs/assets/img/model.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/docs/assets/img/model.png -------------------------------------------------------------------------------- /docs/documentation.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/docs/documentation.html -------------------------------------------------------------------------------- /docs/file_formats.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/docs/file_formats.md -------------------------------------------------------------------------------- /docs/index.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/docs/index.md -------------------------------------------------------------------------------- /docs/notebooks.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/docs/notebooks.html -------------------------------------------------------------------------------- /docs/quickstart.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/docs/quickstart.html -------------------------------------------------------------------------------- /notebooks/.gitkeep: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /notebooks/estimate-growth-rates.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/notebooks/estimate-growth-rates.ipynb -------------------------------------------------------------------------------- /prescient/.gitkeep: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /prescient/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/prescient/__init__.py -------------------------------------------------------------------------------- /prescient/__main__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/prescient/__main__.py -------------------------------------------------------------------------------- /prescient/__pycache__/train.cpython-37.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/prescient/__pycache__/train.cpython-37.pyc -------------------------------------------------------------------------------- /prescient/__pycache__/veres.cpython-37.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/prescient/__pycache__/veres.cpython-37.pyc -------------------------------------------------------------------------------- /prescient/commands/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/prescient/commands/__init__.py -------------------------------------------------------------------------------- /prescient/commands/perturbation_analysis.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/prescient/commands/perturbation_analysis.py -------------------------------------------------------------------------------- /prescient/commands/process_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/prescient/commands/process_data.py -------------------------------------------------------------------------------- /prescient/commands/simulate_trajectories.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/prescient/commands/simulate_trajectories.py -------------------------------------------------------------------------------- /prescient/commands/train_model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/prescient/commands/train_model.py -------------------------------------------------------------------------------- /prescient/perturb/__init__.py: -------------------------------------------------------------------------------- 1 | from .pert import * 2 | -------------------------------------------------------------------------------- /prescient/perturb/pert.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/prescient/perturb/pert.py -------------------------------------------------------------------------------- /prescient/simulate/__init__.py: -------------------------------------------------------------------------------- 1 | from .sim import * 2 | -------------------------------------------------------------------------------- /prescient/simulate/sim.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/prescient/simulate/sim.py -------------------------------------------------------------------------------- /prescient/train/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/prescient/train/__init__.py -------------------------------------------------------------------------------- /prescient/train/model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/prescient/train/model.py -------------------------------------------------------------------------------- /prescient/train/run.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/prescient/train/run.py -------------------------------------------------------------------------------- /prescient/train/util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/prescient/train/util.py -------------------------------------------------------------------------------- /prescient/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/prescient/utils.py -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/pyproject.toml -------------------------------------------------------------------------------- /setup.cfg: -------------------------------------------------------------------------------- 1 | [metadata] 2 | license_files = LICENSE.txt 3 | -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gifford-lab/prescient/HEAD/setup.py --------------------------------------------------------------------------------