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Related Experiment Video

Updated: Jan 17, 2026

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Published on: November 7, 2025

Robust software development practices improve citations of RNA-seq tools.

Sanskruti Sharma, Ecem Ilgun, Tuna Okcu

Biorxiv : the Preprint Server for Biology

|September 18, 2025

Summary

This summary is machine-generated.

Rigorous software development practices are crucial for RNA sequencing (RNA-seq) tools. Studies show that well-developed RNA-seq software is more widely adopted and cited in scientific research.

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Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Published on: August 4, 2016

Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

RNA sequencing (RNA-seq) is vital for transcriptomic analysis in biology and medicine.
The increasing number of RNA-seq tools requires robust development and distribution practices.
Ensuring software reliability, transparency, and reproducibility is essential for scientific trust.

Purpose of the Study:

To assess the development, maintenance, and distribution of RNA-seq tools.
To identify factors influencing the adoption and dependability of RNA-seq software.
To establish a link between software development practices and tool adoption.

Main Methods:

A comprehensive assessment of 434 RNA-seq tools developed between 2008 and 2024.
Categorization of tools based on analysis type.
Evaluation of development methodologies, distribution, and adoption attributes (e.g., package managers, containerization, documentation).

Main Results:

A significant positive association was found between rigorous software development practices and RNA-seq tool adoption, measured by citations (p < 2.2e-16).
Key characteristics contributing to widespread adoption include package manager availability, containerization, multithreading, documentation quality, and example datasets.
The study provides the first documented evidence linking software quality to tool usage in the RNA-seq field.

Conclusions:

Rigorous software development practices are strongly correlated with the adoption and impact of RNA-seq tools.
Identifying characteristics of successful software can guide the development of more robust and user-friendly tools.
The findings support the need for community-wide standards in RNA-seq software development to enhance reliability and reproducibility.