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. 2024 Sep 2;3(5):e238.
doi: 10.1002/imt2.238. eCollection 2024 Oct.

Sangerbox 2: Enhanced functionalities and update for a comprehensive clinical bioinformatics data analysis platform

Di Chen  1 , Lixia Xu  2 , Huiwu Xing  3 , Weitao Shen  4 , Ziguang Song  5 , Hongjiang Li  1 , Xuqiang Zhu  1 , Xueyuan Li  1 , Lixin Wu  1 , Henan Jiao  1 , Shuang Li  4 , Jing Yan  6 , Yuting He  7 , Dongming Yan  1
Affiliations

Sangerbox 2: Enhanced functionalities and update for a comprehensive clinical bioinformatics data analysis platform

Di Chen et al. Imeta. .

Abstract

In recent years, development in high-throughput sequencing technologies has experienced an increasing application of statistics, pattern recognition, and machine learning in bioinformatics analyses. SangeBox platform to meet different scientific demands. The new version of Sangs is a widely used tool among many researchers, which encourages us to continuously improve the plerBox 2 (http://vip.sangerbox.com) and extends and optimizes the functions of interactive graphics and analysis of clinical bioinformatics data. We introduced novel analytical tools such as random forests and support vector machines, as well as corresponding plotting functions. At the same time, we also optimized the performance of the platform and fixed known problems to allow users to perform data analyses more quickly and efficiently. SangerBox 2 improved the speed of analysis, reduced resource required for computer performance, and provided more analysis methods, greatly promoting the research efficiency.

Keywords: batch analysis; bioinformatics; data processing; web server.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Overview of SangerBox 2. (A) SangerBox's user‐friendly accessibility is underpinned by a robust foundation of diverse data integration, validated analytical methods, expeditious and rational cloud computing services, state‐of‐the‐art online visualization techniques, and trustworthy cloud storage solutions. (B) The standard workflow encompasses a sequence of steps. Initially, users are prompted to upload or select data, with the flexibility to opt for publicly available data sets or to submit their proprietary data. Subsequently, they are invited to choose methodologies, set parameters, and preprocess the data. Upon completion of the analysis facilitated by the analytical tools, users are then able to peruse, select, and download the outcomes pertinent to their research needs. Ultimately, with plotting tools or the acquired results, users are endowed with a suite of conventional graphical representations that can be interactively tailored to their specifications.
Figure 2
Figure 2
Random forest tool analysis case.
Figure 3
Figure 3
Platform's newly update plotting tool. (A) Results from the platform's newly added general plotting tool. (B) The brand new complex heatmap tool. (C) Interactive adjustment functionality within the complex heatmap tool.
See this image and copyright information in PMC

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