CFViSA: A comprehensive and free platform for visualization and statistics in omics-data

Ningqi Wang; Yarong Li; Shuwen Han; Yaozhong Zhang; Jun Yang; Zheng Yin; Cong Deng; Zijing Liu; Yinhang Wu; Wei Wu; Wei Xue; Tianjie Yang; Yangchun Xu; Qirong Shen; Gaofei Jiang; Zhong Wei

doi:10.1016/j.compbiomed.2024.108206

CFViSA: A comprehensive and free platform for visualization and statistics in omics-data

Comput Biol Med. 2024 Mar:171:108206. doi: 10.1016/j.compbiomed.2024.108206. Epub 2024 Feb 28.

Authors

Ningqi Wang¹, Yarong Li², Shuwen Han³, Yaozhong Zhang⁴, Jun Yang⁵, Zheng Yin⁶, Cong Deng⁷, Zijing Liu⁸, Yinhang Wu⁹, Wei Wu¹⁰, Wei Xue¹¹, Tianjie Yang¹², Yangchun Xu¹³, Qirong Shen¹⁴, Gaofei Jiang¹⁵, Zhong Wei¹⁶

Affiliations

¹ Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China. Electronic address: wangnq@njau.edu.cn.
² Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China. Electronic address: liyarong@stu.njau.edu.cn.
³ China Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, China; Key Laboratory of Multiomics Research and Clinical Transformation of Digestive Cancer, China. Electronic address: shuwenhan985@163.com.
⁴ Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China. Electronic address: yaozhongzyz@stu.njau.edu.cn.
⁵ Shanghai Biozeron Biotechnology Co., Ltd., Shanghai, China. Electronic address: yangjun@biozeron.com.
⁶ Shanghai Biozeron Biotechnology Co., Ltd., Shanghai, China.
⁷ Shanghai Biozeron Biotechnology Co., Ltd., Shanghai, China. Electronic address: dengcong@vgenomics.cn.
⁸ Shanghai Biozeron Biotechnology Co., Ltd., Shanghai, China. Electronic address: liuzijing@biozeron.com.
⁹ China Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, China; Key Laboratory of Multiomics Research and Clinical Transformation of Digestive Cancer, China. Electronic address: bawnywuyinhang@163.com.
¹⁰ China Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, China; Key Laboratory of Multiomics Research and Clinical Transformation of Digestive Cancer, China. Electronic address: hchwuwei2018@126.com.
¹¹ College of Artificial Intelligence, Nanjing Agricultural University, Nanjing, 210095, China. Electronic address: xwsky@njau.edu.cn.
¹² Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China. Electronic address: tjyang@njau.edu.cn.
¹³ Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China. Electronic address: ycxu@njau.edu.cn.
¹⁴ Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China. Electronic address: shenqirong@njau.edu.cn.
¹⁵ Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China. Electronic address: gjiang@njau.edu.cn.
¹⁶ Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China. Electronic address: weizhong@njau.edu.cn.

PMID: 38430745
DOI: 10.1016/j.compbiomed.2024.108206

Abstract

Introduction: The rapid growth of omics technologies has led to the use of bioinformatics as a powerful tool for unravelling scientific puzzles. However, the obstacles of bioinformatics are compounded by the complexity of data processing and the distinct nature of omics data types, particularly in terms of visualization and statistics.

Objectives: We developed a comprehensive and free platform, CFViSA, to facilitate effortless visualization and statistical analysis of omics data by the scientific community.

Methods: CFViSA was constructed using the Scala programming language and utilizes the AKKA toolkit for the web server and MySQL for the database server. The visualization and statistical analysis were performed with the R program.

Results: CFViSA integrates two omics data analysis pipelines (microbiome and transcriptome analysis) and an extensive array of 79 analysis tools spanning simple sequence processing, visualization, and statistics available for various omics data, including microbiome and transcriptome data. CFViSA starts from an analysis interface, paralleling a demonstration full course to help users understand operating principles and scientifically set the analysis parameters. Once analysis is conducted, users can enter the task history interface for figure adjustments, and then a complete series of results, including statistics, feature tables and figures. All the graphic layouts were printed with necessary statistics and a traceback function recording the options for analysis and visualization; these statistics were excluded from the five competing methods.

Conclusion: CFViSA is a user-friendly bioinformatics cloud platform with detailed guidelines for integrating functions in multi-omics analysis with real-time visualization adjustment and complete series of results provision. CFViSA is available at http://www.cloud.biomicroclass.com/en/CFViSA/.

Keywords: Bioinformatics; Comprehensive platform; Omics data; Statistics; User-friendly; Visualization.

MeSH terms

Computational Biology* / methods
Databases, Factual
Gene Expression Profiling* / methods
Software
Transcriptome