benchmarking gene regulatory networks
Project description
bengrn
Awesome Benchmark of Gene Regulatory Networks created by @jkobject
The package is supposed to work with GRnnData It can run Genie3 & pyscenic on your data as a comparison
It has 4 different types of key ground truth data to compare your GRN to:
- sushmita roy's ChIP+Perturb ground truth
- collectri's literature curated ground truth
- dorothea's literature curated ground truth
- tf2gene's chip curated ground truth
You can find the documentation here
Install it from PyPI
pip install bengrn
Usage
from bengrn import BenGRN
from bengrn import some_test_function
# a GRN in grnndata formart
grndata
BenGRN(grndata).do_tests()
#or
some_test_function(grndata)
see more in the notebooks in the docs folder or in the documentation
Development
Read the CONTRIBUTING.md file.
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