强大的软件开发实践改善了RNA-seq工具的引用
bioRxiv : the preprint server for biology
|September 18, 2025
概括
严格的软件开发实践对于RNA测序 (RNA-seq) 工具至关重要. 研究表明,开发完善的RNA-seq软件在科学研究中得到了更广泛的采用和引用.
科学领域:
- 生物信息学是一种生物信息学.
- 计算生物学 计算生物学
- 基因组学就是基因组学.
背景情况:
- RNA测序 (RNA-seq) 对于生物学和医学中的转录组分析至关重要.
- 越来越多的RNA-seq工具需要强大的开发和分销实践.
- 确保软件的可靠性,透明度和可重复性对于科学信任至关重要.
研究的目的:
- 评估RNA-seq工具的开发,维护和分发.
- 确定影响RNA-seq软件的采用和可靠性的因素.
- 建立软件开发实践与工具采用之间的联系.
主要方法:
- 2008年至2024年间开发的434个RNA-seq工具的综合评估.
- 基于分析类型的工具分类.
- 开发方法,分发和采用属性的评估 (例如,包管理器,集装箱,文档).
主要成果:
- 在严格的软件开发实践和RNA-seq工具的采用之间发现了显著的积极关联,通过引用来衡量 (p < 2.2e-16).
- 有助于广泛采用的关键特征包括包管理器的可用性,容器化,多线程,文档质量和示例数据集.
- 该研究提供了第一个证据证据,将软件质量与RNA-seq领域的工具使用联系起来.
结论:
- 严格的软件开发实践与RNA-seq工具的采用和影响密切相关.
- 识别成功软件的特征可以指导开发更强大,更易于使用的工具.
- 这些发现支持在RNA-seq软件开发中需要全社区标准,以提高可靠性和可重复性.
相关概念视频
Ribosome Profiling
4.1K
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
4.1K
RNA-seq
11.8K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
11.8K
RNA Polymerase II Accessory Proteins
3.8K
3.8K
Sanger Sequencing
773.3K
DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
773.3K
Improving Translational Accuracy
14.1K
Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
14.1K
Improving Translational Accuracy
3.6K
3.6K


