DoubletDetection

https://doubletdetection.readthedocs.io

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

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### Install DoubletDetection via PyPI

Source: https://doubletdetection.readthedocs.io

Standard installation command for the package.

```bash
pip install doubletdetection
```

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### Install DoubletDetection from Source

Source: https://doubletdetection.readthedocs.io

Commands to clone the repository and install the package locally.

```bash
git clone https://github.com/JonathanShor/DoubletDetection.git
cd DoubletDetection
pip3 install .
```

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### Install via Pipenv

Source: https://doubletdetection.readthedocs.io

Alternative installation command for environments using pipenv to handle custom dependencies.

```bash
pipenv run pip3 install .
```

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### Run Basic Doublet Classification

Source: https://doubletdetection.readthedocs.io

Workflow for initializing the classifier, fitting the model to a count matrix, and generating doublet labels and scores.

```python
import doubletdetection
clf = doubletdetection.BoostClassifier()
# raw_counts is a cells by genes count matrix
labels = clf.fit(raw_counts).predict()
# higher means more likely to be doublet
scores = clf.doublet_score()
```

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