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.
Please check out instead the new repo cytograph2.
The following instructions should work for Linux and Mac (unfortunately, we have no experience with Windows).
-
Install Anaconda, Python 3.6 version
-
Install
loompy:
git clone https://github.com/linnarsson-lab/Loom.git
cd Loom/python
python setup.py install
- Install
cytograph:
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
Make sure bhtsne is in your $PATH
Note: pipelines are now separated out into their own repos: