Algorithms for single-cell analysis
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What's this?

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).

  1. Install Anaconda, Python 3.6 version

  2. Install loompy:

git clone
cd Loom/python
python install
  1. Install cytograph:
git clone
cd cytograph/bhtsne
g++ sptree.cpp tsne.cpp -o bh_tsne -O2
cd ..
python install

Make sure bhtsne is in your $PATH

Running the pipeline

Note: pipelines are now separated out into their own repos: