Usage
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:
Selection
The central class for probe set selection:
selector = sp.se.ProbesetSelector(adata)
selector.select_probeset()
selected_probeset = selector.probeset.index[selector.probeset["selection"]].to_list()
Evaluation
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.