Baize, a web-based software tool for rapid evaluation of sample contamination in three critical dimensions: platelet contamination, erythrocyte lysis, and residual coagulation protein carryover. The algorithm calculates cell-type-specific contamination indices by normalizing the summed intensity of marker proteins against the total intensity of plasma proteome (Contamination Index = Marker Protein Intensities / Σ All Plasma Protein Intensities). Users can submit a protein matrix with a sample annotation table, and then Baize will output an evaluation of contamination for every plasma sample. Baize is freely accessible at https://www.guomics.com/Baize.

Output

The output provides each sample contamination profile, enabling rapid quality control decisions without requiring manual intervention.

Installation

If you want to use Baize by source code, you can install python and install requirements package.

Prerequisites

Please make sure you have a valid installation of conda or miniconda. We recommend setting up miniconda as described on their website.

git clone https://github.com/guomics-lab/Baize.git
cd Baize

conda create -n Baize python=3.9
conda activate Baize

pip install -r requirements.txt

Run

python web_main.py

Open your browser and go to http://127.0.0.1:5000/Baize