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.