benchmarking gene regulatory networks
Project description
bengrn
Benchmark your gene regulatory networks inference algorithm (from scRNAseq or bulk RNAseq dataset) with BenGRN
The package is supposed to work with GRnnData and only uses biological ground truth datasets.
It can run Genie3 & pyscenic on your data as a comparison
It has 3 main different types of key ground truth data to compare your GRN to:
- Mc Calla et al.'s ChIP+Perturb ground truth
- omnipath's literature curated ground truth
- genome wide perturb seq 's dataset
You can find the documentation here
Install it from PyPI
pip install bengrn
Install it locally and run the notebooks:
git clone https://github.com/jkobject/benGRN.git
pip install -e 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 the notebooks in docs:
Development
Read the CONTRIBUTING.md file.
Awesome Benchmark of Gene Regulatory Networks created by @jkobject
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