ArticleNAR genomics and bioinformatics2025
Varan: a tool for managing mutational data and creating cancer studies in cBioPortal.
Article in NAR genomics and bioinformatics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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9 authors.
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Abstract
cBioPortal has established itself as a widely used platform for exploring and visualizing multidimensional cancer data. Additionally, users have the option to upload their own cancer study for a comprehensive experience. However, the uploading step can be challenging due to the numerous files required by the platform, as well as the meticulous review of genomic alterations that need to be included in the study. Therefore, there is an increasing need for efficient data management solutions to facilitate the creation of studies in cBioPortal and optimize user experience by streamlining research workflows. In this application note, we present Varan, an innovative data management tool developed to help users at the initial stage of cancer genomic studies' upload, enhancing the data preparation process. Varan addresses challenges related to data formatting, filtering variants based on annotation, metadata file creation, quality checks, and study versioning, thereby enabling researchers to shorten the preparation process time and have control over the type of data to be uploaded to cBioPortal. In conclusion, Varan significantly improves the efficiency and accuracy of preparing cancer genomic studies for cBioPortal, ultimately enhancing the user experience and advancing cancer research through streamlined data management.
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