RNA-protein interaction predictions without high-throughput data: an overview and benchmark of in silico tools

This repository contains supplementary files and information for the publication Krautwurst and Lamkiewicz (2024, https://doi.org/10.1101/2024.06.24.600368).

tool_collection.md
Collection of all RPI prediction tools gathered during initial literature research. Contains basic information on each tool and their availability status.

HTS_RPI_tools.md
RPI prediction tools which are focused on the availability or usage of HTS datasets. These were not evaluated in our study, except otherwise noted.

tool_evaluation.xlsx
Evaluation information and results of the evaluated RPI prediction tools in our study.

tool_evaluation-score.md
Reasoning and information on the distribution of evaluation score points for all evaluated tools.

evaluation_table.csv
Evaluation result values from tool_evaluation.xlsx, as csv for further processing/plotting of the data (does not include post-processing potential).

evaluation_table_withppp.csv
Evaluation result values from tool_evaluation.xlsx, as csv for further processing/plotting of the data (includes post-processing potential).

guidetree_tools.pdf/png
Guide tree figure in high resolution.

examples_figure.pdf
Figure of the four investigated biological RPI examples, with the interactions visualized based on the available literature.

evaluation_heatmap.pdf
Evaluation heatmap in high resolution.

plot_heatmap.py
In-house python script for plotting the evaluation_heatmap based on the evaluation_table.csv.