Scrublet

Single-Cell Remover of Doublets

Python code for identifying doublets in single-cell RNA-seq data. For details and validation of the method, see our paper in Cell Systems or the preprint on bioRxiv.

Quick start:

For a typical workflow, including interpretation of predicted doublet scores, see the example notebook.

Given a raw (unnormalized) UMI counts matrix counts_matrix with cells as rows and genes as columns, calculate a doublet score for each cell:

import scrublet as scr
scrub = scr.Scrublet(counts_matrix)
doublet_scores, predicted_doublets = scrub.scrub_doublets()

scr.scrub_doublets() simulates doublets from the observed data and uses a k-nearest-neighbor classifier to calculate a continuous doublet_score (between 0 and 1) for each transcriptome. The score is automatically thresholded to generate predicted_doublets, a boolean array that is True for predicted doublets and False otherwise.

Best practices:

When working with data from multiple samples, run Scrublet on each sample separately. Because Scrublet is designed to detect technical doublets formed by the random co-encapsulation of two cells, it may perform poorly on merged datasets where the cell type proportions are not representative of any single sample.
Check that the doublet score threshold is reasonable (in an ideal case, separating the two peaks of a bimodal simulated doublet score histogram, as in this example), and adjust manually if necessary.
Visualize the doublet predictions in a 2-D embedding (e.g., UMAP or t-SNE). Predicted doublets should mostly co-localize (possibly in multiple clusters). If they do not, you may need to adjust the doublet score threshold, or change the pre-processing parameters to better resolve the cell states present in your data.

Installation:

To install with PyPI:

pip install scrublet

To install from source:

git clone https://github.com/AllonKleinLab/scrublet.git
cd scrublet
pip install -r requirements.txt
pip install --upgrade .

Old versions:

Previous versions can be found here.

Other doublet detection tools:

DoubletFinder
DoubletDecon
DoubletDetection

License

AllonKleinLab/scrublet

ErrorLooks like something went wrong!

About

Resources

License

Uh oh!

Stars

Watchers

Forks

Releases

Packages 0

Languages

Error
Looks like something went wrong!

Packages