Spapros provides functions for gene set selection, evaluation and several visualization utilities. For any selection and evaluation an AnnData object (adata) of a scRNA-seq data set is needed. To combine gene set selection with probe design (pre-filtering of genes and final probe sequence design) we use the spapros package in combination with our probe design package oligo-designer-toolsuite.

Import package

Import the spapros API as follows:

import spapros as sp

You can then access the main classes like this:


The central class for probe set selection:

selector =
selected_probeset = selector.probeset.index[selector.probeset["selection"]].to_list()


The central class for probe set evaluation and comparison:

evaluator = sp.ev.ProbesetEvaluator()
evaluator.evaluate_probeset(adata, selected_probeset)

Probe design

Check out our tutorial End to end selection for a detailed explanation on how to combine gene panel selection and probe design.

More information

  • The quickest way to learn how to use spapros is to follow our Tutorials.

  • For an overview of available functions and detailed information on each function check out the API.

  • If you run into issues or have further questions check out the issue section on github and please raise your question there if no one else has yet.