https://github.com/hisplan/clineage-simulation
This simulates cell lineage using eSTGt, reconstructs the lineage tree based on the mutation table generated by the simulation, and finally outputs various comparison metrics between the simulation and reconstruction.
https://github.com/hisplan/clineage-simulation
human-cell-lineage phylogeny simulation
Last synced: 5 months ago
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This simulates cell lineage using eSTGt, reconstructs the lineage tree based on the mutation table generated by the simulation, and finally outputs various comparison metrics between the simulation and reconstruction.
- Host: GitHub
- URL: https://github.com/hisplan/clineage-simulation
- Owner: hisplan
- Created: 2018-05-30T07:22:49.000Z (about 8 years ago)
- Default Branch: master
- Last Pushed: 2019-05-14T01:54:11.000Z (about 7 years ago)
- Last Synced: 2024-01-29T20:26:12.863Z (over 2 years ago)
- Topics: human-cell-lineage, phylogeny, simulation
- Language: MATLAB
- Homepage:
- Size: 404 MB
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# clineage-simulation
## Prerequisites
- CLineage
- Python 3+
- MATLAB 2017
- [eSTGt](https://github.com/hisplan/eSTGt) 1.1
- [TreeCmp](https://eti.pg.edu.pl/treecmp/index.html) v2.0
- TMC
## Installation
This will download and install TreeCmp and eSTGt:
```bash
$ ./install.sh
```
## Configuration
Use a proper config file for your environment:
- `config.math102-lx.env` for math102-lx
- `config.windows.env` for Windows
- `config.mac.env` for Mac OS X
or you can create a new `.env` file for your own environment.
## Run Simulator
```bash
$ python simulator.py \
--env config.math102-lx.env \
--project ~/clineage-simulation/example/example-01 \
--config config.json
```
## For Developers
### Updating Mutation Transition Table
- Update `om6_ms_only_ac_28x28.csv`.
- Update and run `prepare.m`.
- If the matrix size changes, there are some hardcoded number such as 28 in `run_simul.m` and `adjust_ms_mutation_transition_prob.m`.
### To Do
- maybe decouple from clineage to be runnable totally independently.
- maybe use MATLAB API for Python