benchmarking gene regulatory networks
Reason this release was yanked:
issues
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 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 more in the notebooks in the docs folder or in the documentation
Development
Read the CONTRIBUTING.md file.
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
bengrn-1.0.0.tar.gz
(52.1 kB
view details)
Built Distribution
bengrn-1.0.0-py3-none-any.whl
(56.6 kB
view details)
File details
Details for the file bengrn-1.0.0.tar.gz.
File metadata
- Download URL: bengrn-1.0.0.tar.gz
- Upload date:
- Size: 52.1 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via: poetry/1.6.1 CPython/3.11.4 Linux/5.15.0-107-generic
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 1768ce42aae4d71fef60c0019539d2273736826538ca15cb15caee65bb556560 |
|
| MD5 | 83681ad5d1c729da85904ddc031f25c1 |
|
| BLAKE2b-256 | 707637a8c6e0e4379c101514f694836e2559986a5716ca1037c9371c34f33cff |
File details
Details for the file bengrn-1.0.0-py3-none-any.whl.
File metadata
- Download URL: bengrn-1.0.0-py3-none-any.whl
- Upload date:
- Size: 56.6 kB
- Tags: Python 3
- Uploaded using Trusted Publishing? No
- Uploaded via: poetry/1.6.1 CPython/3.11.4 Linux/5.15.0-107-generic
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | f5f040137c0750d1c5453ce8e478c81495834de9fa4a82e496adf9df9e61f059 |
|
| MD5 | 1fda64047fc9de4a73fec4fd36096331 |
|
| BLAKE2b-256 | ccdf5813935065b70bb4ccf96bdb2bd9c9e9e9441315425b00d4a3637790da32 |
