outbreak.info R package
with the outbreak.info teamAbout the project:
outbreak.info tracks daily developments in SARS-CoV-2 variants, COVID-19 cases and deaths, and emerging research (including publications, clinical trials, datasets, and more). This R pacakge provides data access to the SARS-CoV-2 variant data, COVID-19 cases and deaths data, and research metadata standardized by outbreak.info.
View the project
outbreak-info.github.io/R-outbreak-info/
Publications
Karthik Gangavarapu, Alaa Abdel Latif, Julia L. Mullen, Manar Alkuzweny, Emory Hufbauer, Ginger Tsueng, Emily Haag, Mark Zeller, Christine M. Aceves, Karina Zaiets, Marco Cano, Xinghua Zhou, Zhongchao Qian, Rachel Sattler, Nathaniel L. Matteson, Joshua I. Levy, Raphael T. C. Lee, Lucas Freitas, Sebastian Maurer-Stroh, GISAID Core and Curation Team, Marc A. Suchard, Chunlei Wu, Andrew I. Su, Kristian G. Andersen & Laura D. Hughes. Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations. Nat Methods (2023). https://doi.org/10.1038/s41592-023-01769-3
Ginger Tsueng, Julia L. Mullen, Manar Alkuzweny, Marco Cano, Benjamin Rush, Emily Haag, Jason Lin, Dylan J. Welzel, Xinghua Zhou, Zhongchao Qian, Alaa Abdel Latif, Emory Hufbauer, Mark Zeller, Kristian G. Andersen, Chunlei Wu, Andrew I. Su, Karthik Gangavarapu & Laura D. Hughes. Outbreak.info Research Library: a standardized, searchable platform to discover and explore COVID-19 resources. Nat Methods (2023). https://doi.org/10.1038/s41592-023-01770-w
Data sources
Data sources can be viewed on outbreak.info.
Code
