Preprocessing

Contents

Preprocessing#

Guide Assignment#

Guide assignment is essential for quality control in single-cell Perturb-seq data, ensuring accurate mapping of guide RNAs to cells for reliable interpretation of gene perturbation effects. pertpy provides a simple function to assign guides based on thresholds and a Gaussian mixture model [RSP+22].

preprocessing.GuideAssignment

Assign cells to guide RNAs.

Example implementation:

import pertpy as pt
import scanpy as sc

mdata = pt.dt.papalexi_2021()
gdo = mdata.mod["gdo"]
gdo.layers["counts"] = gdo.X.copy()
sc.pp.log1p(gdo)

ga = pt.pp.GuideAssignment()
ga.assign_by_threshold(gdo, 5, layer="counts", output_layer="assigned_guides")

ga.plot_heatmap(gdo, layer="assigned_guides")

See guide assignment tutorial.

Contents