Skip to main content

Inferelator: Network Inference

Project description

Inferelator 3.0

PyPI version CI codecov Documentation Status

The Inferelator 3.0 is a package for gene regulatory network inference that is based on regularized regression. It is an update of the Inferelator 2.0, which is an update of the original Inferelator It is maintained by the Bonneau lab in the Systems Biology group of the Flatiron Institute.

This repository is the actively developed inferelator package for python. It works for both single-cell and bulk transcriptome experiments. Includes AMuSR (Castro et al 2019), elements of InfereCLaDR (Tchourine et al 2018), and single-cell workflows (Jackson et al 2020).

We recommend installing this package from PyPi using python -m pip install inferelator. If running locally, also install pathos by python -m pip install pathos for parallelization. If running on a cluster, also install dask by python -m pip install dask[complete] dask_jobqueue for dask-based parallelization.

This package can also be installed from the github repository. Clone the inferelator GitHub repository and run python setup.py install.

Documentation is available at https://inferelator.readthedocs.io, and basic workflows for Bacillus subtilis and Saccharomyces cerevisiae are included with a tutorial.

All current example data and scripts are available from Zenodo DOI.

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

inferelator-0.5.8.tar.gz (108.7 kB view hashes)

Uploaded source

Built Distribution

inferelator-0.5.8-py3-none-any.whl (132.5 kB view hashes)

Uploaded py3

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Huawei Huawei PSF Sponsor Microsoft Microsoft PSF Sponsor NVIDIA NVIDIA PSF Sponsor Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page