To promote the reproducibility of results presented in biomedical publications, we developed BioVisReport for rapidly generating of an interactive website based on a user-defined Markdown file. Researchers can attach the website address to their publication, allowing readers conveniently reproduce research findings and perform further analyses, thus maximizing the values of biomedical data associated with a peer-reviewed publication.

Currently, BioVisReport offers nineteen basic plots, and the excellent extensibility supporting flexible integration of user-developed Python plugins with R/JavaScript/Python/Julia code. An interactive website generated by this tool is described in detail in the supplementary data and available at https://github.com/biovis-report. Importantly, BioVisReport has been used by external researchers to construct the data portal in their paper published in Nature Communication (https://www.nature.com/articles/s41467-020-19342-3), further demonstrating the utility of our tool in the biomedical peer-reviewed publications.

You can clone the example repo to taste the biovis-report.

To better demonstrate the capabilities of BioVisReport, we provide an example based on the genomic and transcriptomic profiling of the Chinese Triple-Negative Breast Cancer cohort (Jiang, et al., Cancer Cell, 2019).