FigureYa: A Standardized Visualization Framework for Enhancing Biomedical Data Interpretation and Research Efficiency
iMetaMed, vol. 1
Abstract
ABSTRACT Biomedical research data visualization faces several challenges, including insufficient expertise and fragmented methodologies, which severely limit research efficiency and result quality. FigureYa is a standardized visualization framework composed of 317 modular R/python scripts, rather than a standalone software or desktop application. It covers key domains such as expression profiling, immune analysis, survival analysis, and single‐cell data visualization. Based on the concept of “replace data and use,” FigureYa significantly lowers the technical threshold, allowing researchers to generate high‐quality charts without requiring an extensive programming background. Compared to generic online R code snippets, FigureYa offers rigorously developed, thoroughly validated, and biologically contextualized visualization modules originally written by the author team. Each script includes version‐matched environments, example datasets, and detailed annotations, providing clear advantages in automation, reproducibility, and scientific professionalism, thereby providing a standardized visualization solution for complex biomedical data. This innovative tool optimizes research time allocation, promotes interdisciplinary collaboration, accelerates scientific discovery and clinical translation, and provides robust data visualization support for biomedical research.
Authors 47
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Centre National de la Recherche Scientifique · Inserm · Institut de génétique et de biologie moléculaire et cellulaire · Université de Strasbourg
Affiliation as printed
Department of Cancer and Functional Genomics, Institute of Genetics and Molecular and Cellular Biology CNRS/INSERM/UNISTRA Illkirch France
Department of Cancer and Functional Genomics, Institute of Genetics and Molecular and Cellular Biology, CNRS/INSERM/UNISTRA, Illkirch, France
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Zhujiang Hospital · Southern Medical University
Affiliation as printed
Department of Oncology, Zhujiang Hospital Southern Medical University Guangzhou Guangdong China
Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
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Chinese PLA General Hospital · Chinese People's Liberation Army
Affiliation as printed
State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology, Department of Hematology Fifth Medical Center, Chinese PLA General Hospital Beijing China
State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology, Department of Hematology, Fifth Medical Center, Chinese PLA General Hospital, Beijing, China
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Zhujiang Hospital · Southern Medical University
Affiliation as printed
Department of Oncology, Zhujiang Hospital Southern Medical University Guangzhou Guangdong China
Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
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Affiliation as printed
The University of Chicago Chicago Illinois USA
The University of Chicago, Chicago, Illinois, USA
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Capital Medical University · Beijing Chao-Yang Hospital, Capital Medical University
Affiliation as printed
Department of Thyroid and Neck Surgery, Beijing Chaoyang Hospital Capital Medical University Beijing China
Department of Thyroid and Neck Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
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Ningbo University · Chinese Academy of Sciences · Center for Excellence in Molecular Plant Sciences
Affiliation as printed
CAS Center for Excellence in Molecular Plant Sciences (CEMPS) Shanghai China
Institute of Plant Virology Ningbo University Ningbo Zhejiang China
CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Shanghai, China
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Affiliation as printed
Ferring Pharmaceuticals (Shanghai) Co., Ltd. Shanghai China
School of Life Sciences Westlake University Hangzhou Zhejiang China
Westlake Laboratory of Life Sciences and Biomedicine Hangzhou Zhejiang China
School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
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Affiliation as printed
Institute of Cancer Stem Cell Dalian Medical University Dalian Liaoning China
Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, China
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Shandong Provincial Hospital · Zhujiang Hospital · Chinese People's Liberation Army · Shandong First Medical University · Southern Medical University
Affiliation as printed
Department of Hematology Shandong Provincial Hospital Affiliated to Shandong First Medical University Jinan Shandong China
Department of Oncology, Zhujiang Hospital Southern Medical University Guangzhou Guangdong China
Department of Vascular Neurosurgery, New Era Stroke Care and Research Institute The PLA Rocket Force Characteristic Medical Center Beijing China
Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
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Zhujiang Hospital · Southern Medical University
Affiliation as printed
Department of Oncology, Zhujiang Hospital Southern Medical University Guangzhou Guangdong China
Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
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Zhujiang Hospital · Southern Medical University
Affiliation as printed
Department of Oncology, Zhujiang Hospital Southern Medical University Guangzhou Guangdong China
Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
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Zhujiang Hospital · Southern Medical University
Affiliation as printed
Department of Oncology, Zhujiang Hospital Southern Medical University Guangzhou Guangdong China
Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
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Affiliation as printed
State Key Laboratory of Tree Genetics and Breeding, Co‐Innovation Center for Sustainable Forestry in Southern China Nanjing Forestry University Nanjing Jiangsu China
State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China
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Nanfang Hospital · Southern Medical University · South China University of Technology
Affiliation as printed
Cancer Center, the Sixth Affiliated Hospital, School of Medicine South China University of Technology Foshan Guangdong China
Department of Oncology, Nanfang Hospital Southern Medical University Guangzhou Guangdong China
Foshan Key Laboratory of Translational Medicine in Oncology, the Sixth Affiliated Hospital, School of Medicine South China University of Technology Foshan Guangdong China
Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
Foshan Key Laboratory of Translational Medicine in Oncology, the Sixth Affiliated Hospital, School of Medicine, South China University of Technology, Foshan, Guangdong, China
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National Institutes of Health · University of Macau · National Cancer Institute · Center for Cancer Research
Affiliation as printed
Faculty of Health Sciences University of Macau Macau Macau SAR China
Present Address: Thoracic Surgery Branch Thoracic Surgery Branch, Center for Cancer Research, NCI, NIH, Bethesda Maryland USA
Faculty of Health Sciences, University of Macau, Macau, Macau SAR, China
Present Address: Thoracic Surgery Branch, Thoracic Surgery Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, USA
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The Affiliated Yongchuan Hospital of Chongqing Medical University
Affiliation as printed
Department of Breast and Thyroid Surgery The First Affiliated Hospital of Chongqing Medical University Chongqing China
Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Affiliation as printed
School of Life Sciences and Technology Tongji University Shanghai China
School of Life Sciences and Technology, Tongji University, Shanghai, China
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Capital Institute of Pediatrics · Children's Hospital of Capital Institute of Pediatrics
Affiliation as printed
Department of General Surgery Capital Institute of Pediatrics Affiliated Children's Hospital Beijing China
Department of General Surgery, Capital Institute of Pediatrics Affiliated Children's Hospital, Beijing, China
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Shanghai Medical College of Fudan University · Fudan University · Zhongshan Hospital
Affiliation as printed
Department of Thoracic Surgery, Zhongshan Hospital Fudan University Shanghai China
Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
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Affiliation as printed
Ferring Pharmaceuticals (Shanghai) Co., Ltd. Shanghai China
School of Life Sciences Westlake University Hangzhou Zhejiang China
Westlake Laboratory of Life Sciences and Biomedicine Hangzhou Zhejiang China
Ferring Pharmaceuticals (Shanghai) Co., Ltd., Shanghai, China
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Wuhan Union Hospital · Huazhong University of Science and Technology
Affiliation as printed
Department of Ultrasound Medicine, Union Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan Hubei China
Hubei Province Clinical Research Center for Medical Imaging Wuhan Hubei China
Hubei Province Key Laboratory of Molecular Imaging Wuhan Hubei China
Department of Ultrasound Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
Hubei Province Clinical Research Center for Medical Imaging, Wuhan, Hubei, China
Hubei Province Key Laboratory of Molecular Imaging, Wuhan, Hubei, China
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Affiliation as printed
Nanjing University Medical School Nanjing Jiangsu China
Nanjing University Medical School, Nanjing, Jiangsu, China
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Second Military Medical University · Shanghai Changzheng Hospital
Affiliation as printed
Department of Gastrointestinal Surgery Second Affiliated Hospital (Changzheng Hospital) of Naval Medical University Shanghai China
Department of Gastrointestinal Surgery, Second Affiliated Hospital (Changzheng Hospital) of Naval Medical University, Shanghai, China
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Shantou University · Cancer Hospital of Shantou University Medical College
Affiliation as printed
Department of Head and Neck Surgery Cancer Hospital of Shantou University Medical College Shantou Guangdong China
Department of Head and Neck Surgery, Cancer Hospital of Shantou University Medical College, Shantou, Guangdong, China
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Shanghai Jiao Tong University · Shanghai First People's Hospital
Affiliation as printed
Department of Neurosurgery, Shanghai General Hospital, School of Medicine Shanghai Jiaotong University Shanghai China
Department of Neurosurgery, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
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Capital Medical University · Beijing Children’s Hospital
Affiliation as printed
Big Data Center, Beijing Children's Hospital Capital Medical University, National Center for Children's Health Beijing China
Big Data Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
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Chinese Academy of Medical Sciences & Peking Union Medical College · Peking Union Medical College Hospital
Affiliation as printed
Center for bioinformatics, National Infrastructures for Translational Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College Beijing China
Center for bioinformatics, National Infrastructures for Translational Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Affiliation as printed
Suichuang Tech Co., Ltd. Guangzhou Guangdong China
Suichuang Tech Co., Ltd., Guangzhou, Guangdong, China
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Affiliation as printed
Institute of Image Processing and Pattern Recognition Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China Shanghai China
Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai, China
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Yufang Wang Aachen
Affiliation as printed
Leiden University Leiden the Netherlands
Leiden University, Leiden, the Netherlands
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Sichuan University · West China Hospital of Sichuan University · State Key Laboratory of Biotherapy
Affiliation as printed
Institute of Breast Health Medicine, State Key Laboratory of Biotherapy, West China Hospital Sichuan University and Collaborative Innovation Center Chengdu Sichuan China
Institute of Breast Health Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
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Second Military Medical University
Affiliation as printed
Department of Phytochemistry, School of Pharmacy Second Military Medical University Shanghai China
Department of Phytochemistry, School of Pharmacy, Second Military Medical University, Shanghai, China
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Shandong Provincial Hospital · Zhujiang Hospital · Chinese People's Liberation Army · Shandong First Medical University · Southern Medical University
Affiliation as printed
Department of Hematology Shandong Provincial Hospital Affiliated to Shandong First Medical University Jinan Shandong China
Department of Oncology, Zhujiang Hospital Southern Medical University Guangzhou Guangdong China
Department of Vascular Neurosurgery, New Era Stroke Care and Research Institute The PLA Rocket Force Characteristic Medical Center Beijing China
Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
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Affiliation as printed
Faculty of Applied Sciences Macao Polytechnic University Macau Macau SAR China
Faculty of Applied Sciences, Macao Polytechnic University, Macau, Macau SAR, China
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Ningbo University · Chinese Academy of Sciences · Center for Excellence in Molecular Plant Sciences
Affiliation as printed
CAS Center for Excellence in Molecular Plant Sciences (CEMPS) Shanghai China
Institute of Plant Virology Ningbo University Ningbo Zhejiang China
Institute of Plant Virology, Ningbo University, Ningbo, Zhejiang, China
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Affiliation as printed
Institute of Cancer Stem Cell Dalian Medical University Dalian Liaoning China
Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, China
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Affiliation as printed
Academy for Advanced Interdisciplinary Studies Peking University Beijing China
Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
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Huazhong Agricultural University
Affiliation as printed
National Key Laboratory of Agricultural Microbiology, College of Resources and Environment Huazhong Agricultural University Wuhan Hubei China
National Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan, Hubei, China
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Albert Einstein College of Medicine
Affiliation as printed
Department of Pathology Albert Einstein College of Medicine Bronx New York USA
Department of Pathology, Albert Einstein College of Medicine, Bronx, New York, USA
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Shanghai Jiao Tong University · Renji Hospital · Shanghai Cancer Institute
Affiliation as printed
State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute & Department of Liver Surgery, Renji Hospital Shanghai Jiao Tong University School of Medicine Shanghai China
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Dalian Medical University · Second Affiliated Hospital of Dalian Medical University
Affiliation as printed
Department of Neurosurgery Second Hospital of Dalian Medical University Dalian Liaoning China
Department of Neurosurgery, Second Hospital of Dalian Medical University, Dalian, Liaoning, China
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Chinese Academy of Medical Sciences & Peking Union Medical College · Peking Union Medical College Hospital
Affiliation as printed
Center for bioinformatics, National Infrastructures for Translational Medicine, Institute of Clinical Medicine & Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College Beijing China
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Tianjin University of Traditional Chinese Medicine
Affiliation as printed
College of Traditional Chinese Medicine Tianjin University of Traditional Chinese Medicine Tianjin China
College of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
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Peng Luo corresponding
Zhujiang Hospital · Southern Medical University
Affiliation as printed
Department of Oncology, Zhujiang Hospital Southern Medical University Guangzhou Guangdong China
Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
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Guangchuang Yu corresponding
Affiliation as printed
Department of Bioinformatics, School of Basic Medical Sciences Southern Medical University Guangzhou Guangdong China
Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
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Ying Ge corresponding
Affiliation as printed
Institute of Cancer Stem Cell Dalian Medical University Dalian Liaoning China
Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, China
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