AmbiQuant: Ambient contamination quantification metrics

• Quantitative ambient contamination-based metrics to evaluate scRNA-seq data quality

• Check out our publication A contamination focused approach for optimizing the single-cell RNA-seq experiment here

• The environment for this pipeline can be installed through the included .yml with the following, which will also initialize a jupyter kernel:

conda env create -f qc_pipe.yml
python -m ipykernel install --user --name=qc_pipe

• this yml file is adapted from QCPipe pipeline published in this protocol

• Follow the steps in ExamplePlots.ipynb to generate ambient contamination metrics plots

• example dataset in the notebook can be downloaded:

  • dropset option:
    make sure you are at the right working directory
    mkdir 5394_YX_2 (make a folder for the files)
    cd 5394_YX_2 (change directory to the folder)
    curl -O -J -L https://www.dropbox.com/sh/1z2nc7v3pp9o286/AACdWSa5uswk1pBLVn9yjhDna?dl=0 (download as a zip file)
    unzip 5394_YX_2.zip (unzip)
  • h5ad option:
    curl -O -J -L https://www.dropbox.com/s/s2h2t5uyd9ygud3/5394_YX_2_full.h5ad?dl=0