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vaeda

vaeda (variaitonal auto-encoder (vae) for doublet annotation (da)) is a python package for doublet annotation in single cell RNA-sequencing. For method details and comparisons to alternative doublet annotation tools, see our pre-print.

Installation

You can install vaeda using conda and pip as follows:

conda create -n vaeda_env python=3.8
conda activate vaeda_env

pip3 install --upgrade tensorflow==2.8.0
pip3 install --upgrade tensorflow-probability==0.16.0
pip3 install 'scanpy[leiden]'==1.8.0
pip3 install typing-extensions==3.7.4 absl-py==0.10 six==1.15.0 wrapt==1.12.1 xlrd==1.2.0
pip3 install -i https://test.pypi.org/simple/ vaeda==0.0.30

Quick Start

import vaeda

...

res = vaeda.vaeda(adata)

Where:

More detailed example

For a more detailed and accessible example, see ./doc/vaeda_scanpy-pbmc3k-tutorial.ipynb, where we modified a tutorial from scanpy (https://scanpy-tutorials.readthedocs.io/en/latest/pbmc3k.html) to illustrate how to use vaeda for doublet annotation.

Other doublet detection tools