https://github.com/border-lab/xftsim
eXtensible Forward Time SIMulator for complex phenogenetic architectures
Science Score: 26.0%
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○CITATION.cff file
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○Scientific vocabulary similarity
Low similarity (12.9%) to scientific vocabulary
Keywords
Repository
eXtensible Forward Time SIMulator for complex phenogenetic architectures
Basic Info
Statistics
- Stars: 2
- Watchers: 2
- Forks: 1
- Open Issues: 0
- Releases: 1
Topics
Metadata Files
README.md
eXtensible Forward Time SIMulator
xftsim simulates complex phenotype/genotype data with an emphasis on short timescale phenomena. xftsim is designed with two primary goals:
make it easy for statistical geneticists to perform reproducible and systematic sensitivity analyses to better understand limitations and assumptions
enable evaulation of methods for analyzing complex traits under realistically complex generative models
Installation
xftsim is on PyPI. It can be installed in a couple minutes using pip and conda:
bash
conda create --name xftsim python=3.9.6
conda activate xftsim
pip install xftsim
Alternatively, you can install the latest development version from github:
bash
git clone https://github/rborder/xftsim
cd xftsim
git checkout dev
pip -e . install
To enable full functionality (i.e., automatic generation of causal diagrams), you must install pygraphviz.
xftsim has been tested on MacOS 13.4 and the following GNU/Linux distributions: Ubuntu 22.04, Ubuntu 24.04, PopOS 22.04, and RHEL 7 using Python version 3.9.6.
`xftsim` depends on the following packages...
``` asciitree==0.3.3 attrs==23.2.0 cattrs==23.2.3 certifi==2023.11.17 cffi==1.17.1 charset-normalizer==3.3.2 chembl-webresource-client==0.10.9 click==8.1.7 cloudpickle==3.1.0 contourpy==1.2.0 csrgraph==0.1.28 cycler==0.12.1 dask==2024.8.0 dask-expr==1.1.10 dask-glm==0.3.2 dask-ml==2024.4.4 Deprecated==1.2.14 distributed==2024.8.0 easydict==1.13 exceptiongroup==1.2.0 fasteners==0.19 fonttools==4.46.0 fsspec==2024.10.0 funcy==2.0 gensim==4.3.2 idna==3.6 importlib-metadata==8.5.0 importlib-resources==6.1.1 iniconfig==2.0.0 jinja2==3.1.4 joblib==1.3.2 kiwisolver==1.4.5 llvmlite==0.39.1 locket==1.0.0 MarkupSafe==3.0.2 matplotlib==3.8.2 msgpack==1.1.0 multipledispatch==1.0.0 networkx==2.8.8 node2vec==0.4.6 nodevectors==0.1.23 nptyping==2.5.0 numba==0.56.4 numcodecs==0.12.1 numpy==1.23.5 packaging==23.2 pandas==2.1.4 pandas-plink==2.2.9 partd==1.4.2 Pillow==10.1.0 platformdirs==4.2.0 pluggy==1.5.0 psutil==6.1.0 pyarrow==18.0.0 pycparser==2.22 pyparsing==3.1.1 pytest==8.3.3 python-dateutil==2.8.2 pytz==2023.3.post1 PyYAML==6.0.2 rdkit==2023.9.5 requests==2.31.0 requests-cache==1.2.0 scikit-learn==1.3.2 scipy==1.11.4 seaborn==0.13.0 sgkit==0.9.0 six==1.16.0 smart-open==7.0.1 sortedcontainers==2.4.0 sparse==0.15.4 tblib==3.0.0 threadpoolctl==3.2.0 tomli==2.0.2 toolz==1.0.0 tornado==6.4.1 tqdm==4.66.2 typing-extensions==4.10.0 tzdata==2023.3 url-normalize==1.4.3 urllib3==2.1.0 wrapt==1.16.0 xarray==2024.7.0 xftsim==0.2.0 zarr==2.18.2 zict==3.0.0 zipp==3.20.2 zstandard==0.23.0 ```Getting started
To get started, check out the documentation!
For a minimal test simulation you can run one of the built in demos (runtime < 1min): ```python3 import warnings warnings.simplefilter(action='ignore', category=FutureWarning)
import xftsim as xft
demo = xft.sim.DemoSimulation('BGRM') demo.run(3)
xft.utils.print_tree(demo.results) ```
Notice
xftsim is under active development. Please let us know if there are features missing or bugs!
GitHub Events
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Last Year
Dependencies
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- funcy ==2.0
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