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
python -m pip install pathos for parallelization.
If running on a cluster, also install
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.