Algorithms for single-cell analysis
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bhtsne
cytograph
.gitignore
README.md
goatools_guide_cellcycle_genes_human.txt
pooling_specification.tab
setup.cfg
setup.py

README.md

cytograph

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.

Installation

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 https://github.com/linnarsson-lab/Loom.git
cd Loom/python
python setup.py install
  1. 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

Running the pipeline

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