gyd1990 / doubletdetection

Doublet detection in single-cell RNA-seq data.

DoubletDetection

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

To install DoubletDetection:

git clone https://github.com/JonathanShor/DoubletDetection.git
cd DoubletDetection
pip3 install --upgrade .

To run basic doublet classification:

import doubletdetection
clf = doubletdetection.BoostClassifier()
# raw_counts is a cells by genes count matrix
labels = clf.fit(raw_counts).predict()

raw_counts is a scRNA-seq count matrix, and must be a 2-dimensional numpy ndarray, with rows being cells. labels is a binary 1-dimensional numpy ndarray with the value 1 representing a detected doublet. The length of labels is equal to the length of raw_counts.

See our jupyter notebook for an example on 8k PBMCs from 10x.

Obtaining data

Data can be downloaded from the 10x website.

Citations

bioRxiv submission is in the works.

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