Skip to main content

Inferelator: Network Inference

Project description

inferelator

Travis codecov Documentation Status

The inferelator is a package for gene regulatory network inference that is based on regularized regression. 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) and elements of InfereCLaDR (Tchourine et al 2018).

To install the python packages needed for the inferelator, run pip install -r requirements.txt. To install the python packages needed for the inferelator multiprocessing functionality, run pip install -r requirements-multiprocessing.txt. To install this package, clone the inferelator GitHub repository and run python setup.py install, or run pip install inferelator.

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.

Files for inferelator, version 0.3.1
Filename, size File type Python version Upload date Hashes
Filename, size inferelator-0.3.1-py3-none-any.whl (93.0 kB) File type Wheel Python version py3 Upload date Hashes View
Filename, size inferelator-0.3.1.tar.gz (71.0 kB) File type Source Python version None Upload date Hashes View

Supported by

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