Awesome
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 (cells by genes), and is array-like. labels
is a binary 1-dimensional numpy ndarray with the value 1 representing a
detected doublet.
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.