This repo contains a collection of algorithms used in our paper "Molecular architecture of the mouse nervous system", currently in review. We provide it here in the interest of transparency and reproducibility. However, we are unable to provide support or documentation for using the code at this time. The instructions below can serve as a starting point.
The following instructions should work for Linux and Mac (unfortunately, we have no experience with Windows).
Install Anaconda, Python 3.6 version
git clone https://github.com/linnarsson-lab/Loom.git cd Loom/python python setup.py install
git clone https://github.com/linnarsson-lab/cytograph.git cd cytograph/bhtsne g++ sptree.cpp tsne.cpp -o bh_tsne -O2 cd .. python setup.py install
bhtsne is in your $PATH
Running the pipeline
Note: pipelines are now separated out into their own repos: