Metadata-Version: 2.1
Name: inferelator
Version: 0.5.0
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
Project-URL: Documentation, https://inferelator.readthedocs.io/
Description: # inferelator 
        
        [![PyPI version](https://badge.fury.io/py/inferelator.svg)](https://badge.fury.io/py/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).
        
        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](https://github.com/flatironinstitute/inferelator) repository and run `python setup.py install`.
        
        Documentation is available at [https://inferelator.readthedocs.io](https://inferelator.readthedocs.io/en/latest/), 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](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
