bio-single-cell-doublet-detection

Scrublet (Python)

Goal: Detect and score doublets in scRNA-seq data using simulated doublet profiles.

Approach: Simulate artificial doublets by combining random cell pairs, embed real and simulated cells together, and score each cell's similarity to simulated doublets.

"Remove doublets from my data" → Identify droplets containing multiple cells by comparing each cell's profile to computationally simulated doublets, then filter flagged cells.

Visualize Doublet Scores

import matplotlib.pyplot as plt

scrub.plot_histogram()
plt.savefig('doublet_histogram.pdf')

## DoubletFinder (R)

**Goal:** Detect doublets in Seurat objects using DoubletFinder's pANN-based classification.

**Approach:** Optimize the pK neighborhood parameter via parameter sweep, compute artificial nearest neighbor proportions, and classify cells as singlets or doublets.