Metadata-Version: 2.1
Name: inferelator
Version: 0.4.0
Summary: Inferelator: Network Inference
Home-page: https://github.com/flatironinstitute/inferelator
Author: Chris Jackson
Author-email: cj59@nyu.edu
Maintainer: Chris Jackson
Maintainer-email: cj59@nyu.edu
License: UNKNOWN
Description: # inferelator 
        
        [![Travis](https://travis-ci.org/flatironinstitute/inferelator.svg?branch=master)](https://travis-ci.org/flatironinstitute/inferelator)
        [![codecov](https://codecov.io/gh/flatironinstitute/inferelator/branch/master/graph/badge.svg)](https://codecov.io/gh/flatironinstitute/inferelator)
        [![Documentation Status](https://readthedocs.org/projects/inferelator/badge/?version=latest)](https://inferelator.readthedocs.io/en/latest/?badge=latest)
        
        The [inferelator](https://doi.org/10.1186/gb-2006-7-5-r36) 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](https://www.simonsfoundation.org/flatiron/center-for-computational-biology/systems-biology/).
        
        This repository is the actively developed inferelator package for python; it works for both single-cell and bulk transcriptome experiments.
        Includes [AMuSR](https://github.com/simonsfoundation/multitask_inferelator/tree/AMuSR/inferelator_ng)  [(Castro et al 2019)](https://doi.org/10.1371/journal.pcbi.1006591),
         elements of [InfereCLaDR](https://github.com/simonsfoundation/inferelator_ng/tree/InfereCLaDR) [(Tchourine et al 2018)](https://doi.org/10.1016/j.celrep.2018.03.048), 
         and single-cell workflows [(Jackson et al 2020)](https://elifesciences.org/articles/51254).
        
        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](https://github.com/flatironinstitute/inferelator) 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](https://zenodo.org/badge/DOI/10.5281/zenodo.3355524.svg)](https://doi.org/10.5281/zenodo.3355524)
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Development Status :: 4 - Beta
Requires-Python: >=3.5
Description-Content-Type: text/markdown
