JonathanShor / DoubletDetection

Doublet detection in single-cell RNA-seq data.

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DoubletDetection is a Python3 package to detect doublets (technical errors) in single-cell RNA-seq count matrices.

Installing DoubletDetection

Install from PyPI

pip install doubletdetection

Install from source

git clone
cd DoubletDetection
pip3 install .

If you are using pipenv as your virtual environment, it may struggle installing from the due to our custom Phenograph requirement. If so, try the following in the cloned repo:

pipenv run pip3 install .

Running DoubletDetection

To run basic doublet classification:

import doubletdetection
clf = doubletdetection.BoostClassifier()
# raw_counts is a cells by genes count matrix
labels =
# higher means more likely to be doublet
scores = clf.doublet_score()
  • raw_counts is a scRNA-seq count matrix (cells by genes), and is array-like
  • labels is a 1-dimensional numpy ndarray with the value 1 representing a detected doublet, 0 a singlet, and np.nan an ambiguous cell.
  • scores is a 1-dimensional numpy ndarray representing a score for how likely a cell is to be a doublet. The score is used to create the labels.

The classifier works best when

  • There are several cell types present in the data
  • It is applied individually to each run in an aggregated count matrix

In v2.5 we have added a new experimental clustering method (scanpy's Louvain clustering) that is much faster than phenograph. We are still validating results from this new clustering. Please see the notebook below for an example of using this new feature.


See our tutorial for an example on 10k PBMCs from 10x Genomics.

Obtaining data

Data can be downloaded from the 10x website.

Credits and citations

Gayoso, Adam, Shor, Jonathan, Carr, Ambrose J., Sharma, Roshan, Pe'er, Dana (2020, December 18). DoubletDetection (Version v3.0). Zenodo.

We also thank the participants of the 1st Human Cell Atlas Jamboree, Chun J. Ye for providing data useful in developing this method, and Itsik Pe'er for providing guidance in early development as part of the Computational genomics class at Columbia University.

This project is licensed under the terms of the MIT license.


Doublet detection in single-cell RNA-seq data.

License:MIT License


Language:Jupyter Notebook 96.5%Language:Python 3.5%