Tinkering with northstar’s internals

The easiest way to understand northstar’s internal code is to use ipython or jupyter notebooks, and use the amazing double question mark magic on the fit method:

import anndata
import northstar

# Read in the GBM data to be annotated
# Here we assume it's a loom file, but
# of course it can be whatever format
newdata = anndata.read_loom('...')

# Prepare the classifier
# We exclude the fetal cells to focus
# on adult tissue. To keep the fetal
# cells, just take away the _nofetal
model = northstar.Subsample(

# Peek inside

This will show you the order of operations. You can use the same double question mark on each of them to understand in detail what’s going on.

Notice also that northstar is a pure Python package. This means that, provided you installed the dependencies, you can download the source code from pypi or GitHub, put into a folder on your machine, add that folder to your PYTHONPATH, and modify the code at will without needing to recompile anything. In fact, you are encouraged to do so and build even better classifiers!