PRADA-RNA_Structuromics

Understanding the spatial organization of biomolecules in living organisms is a central but challenging goal in biology. A nontoxic proximity labeling approach Peroxidase Reactions Activated by D-amino Acids (PRADA) is developed, which uses an engineered oxidase to convert non-proteinogenic D-amino acids into H2O2 for in situ activation of a genetically-fused peroxidase. PRADA is applied in C. elegans, Drosophila, zebrafish, and mice and has unique RNA labeling activity to probe RNA structures in vitro and in vivo. PRADA-RNA_Structuromics shows the analysis for RNA structures from PRADA datasets.

Downstream analysis can be found in analysis.

Software Pre-requisites

1. ShapeMapper2
2. Python
3. R

Installation Requirments

1. snakemake == 7.15.2
2. scipy >= 1.7.1
3. scikit-learn >= 0.24.2
4. numpy <= 1.20.3
5. pandas >= 1.5.0
6. matplotlib >= 3.5.1
7. seaborn >= 0.11.2
8. biopython >= 1.79
9. cairosvg >= 2.7.0
10. statannot >= 0.2.3

This will be automatically done during pip install

Usage

After completing the ShapeMapper2 pipeline, run the notebooks in the analysis/ directory to reproduce the downstream analyses and figures.