northstar¶
Single cell type annotation guided by cell atlases, with freedom to be queer.
Brief description¶
northstar is a Python package to identify cell types within single cell transcriptomics datasets. It uses one or more cell atlases as a baseline and assigns each cell of your dataset to either a known cell type from the atlas(es) or to a novel cluster. northstar’s superpower is that it learn from big data (atlases) but still allows queer cells to make their own cluster if they want to.
northstar was heavily developed during Pride Month.
Installation¶
northstar is a pure Python package, so you can install it using pip:
pip install northstar
To automatically download and use our online atlas collection at https://northstaratlas.github.io/atlas_averages/, you will need to call:
pip install 'northstar[atlas-fetcher]'
Dependencies¶
- numpy
- scipy
- pandas
- scikit-learn
- anndata
- python-igraph>=0.8.0
- leidenalg>=0.8.0
It is recommended that you install python-igraph and leidenalg using pip. However, any installation (e.g. conda) that includes recent enough versions of both packages will work.
Optional deps to use our online atlases:
- requests
- loompy
- scanpy (reduces memory usage)
- pynndescent (only useful if you also use scanpy)
Usage example¶
Also see our Tutorial.
import anndata
import northstar
# Choose an atlas
atlas_name = 'Darmanis_2015'
# Get an AnnData object with the new data to be annotated
new_dataset = anndata.read_loom('...')
# or any other format
# Initialize northstar classes
model = northstar.Averages(
atlas=atlas,
)
# Run the classifier
model.fit(new_dataset)
# Get the cluster memberships for the new cells
membership = model.membership
Citation¶
If you use this software please cite the following paper:
Fabio Zanini*, Bojk A. Berghuis*, Robert C. Jones, Benedetta Nicolis di Robilant, Rachel Yuan Nong, Jeffrey Norton, Michael F. Clarke, Stephen R. Quake. Northstar enables automatic classification of known and novel cell types from tumor samples. Scientific Reports 10, Article number: 15251 (2020), DOI: https://doi.org/10.1038/s41598-020-71805-1
License¶
northstar is released under the MIT license.
NOTE: The module leidenalg, which is a dependency of northstar, is released under the GLP3 license. You agree with those licensing terms if you use leidenalg within northstar.
