Procrustes is a Python package containing tools for transformation of exome-capture-based RNA-Seq gene expression into polyA-like processed RNA-Seq gene expression.
- Operating System: Ubuntu 22.04.1 or compatible Linux distributions
- Python Version: 3.8 or higher
- Hardware: No specific requirements, but a standard computer with enough RAM
- for in-memory operations is necessary.
To install Procrustes, follow these steps. Note that installation may take up to 20 minutes on a standard desktop computer.
git clone https://github.com/BostonGene/Procrustes
cd Procrustes
pip install -e .To run the demo, open the "Demo_run.ipynb" Jupyter notebook and execute all cells. The demo outputs bar plots with CCC (Concordance Correlation Coefficient) values divided into intervals. Completing the demo may take up to 30 minutes on a standard desktop computer.
To analyze your own RNA-Seq expression data with Procrustes, ensure the following:
Your data is calculated utilizing kallisto based on gencode version 23 (Homo Sapiens) and TPM normalized. Transform TPM-expression values using np.log2(exp+1) before analysis. RNA-Seq libraries should be prepared using either the Agilent V4, V7, or V7_UTR library preparation kit. Input the data in the function Procrustes_predict in the format rows x cols. The output will be similar to the demo run, allowing you to compare your results with polyA data of interest.