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refCNV Documentation - Genomic Copy Number Variation (CNV) data from reference samples

refCNV is a represents the subset of the progenetix data for which probe-specific data from genomic array experiments is available.

Citation Options

The refCNV resource and associated data have not been published yet. Articles below refer to the Progenetix and Beacon resources and standards used for implementation.

Huang Q, Carrio-Cordo P, Gao B, Paloots R, Baudis M. (2021) The Progenetix oncogenomic resource in 2021. Database (Oxford). 2021 Jul 17
progenetix.org: Progenetix oncogenomic online resource (2022)
Baudis M, Cleary ML. (2001) Progenetix.net: an online repository for molecular cytogenetic aberration data. Bioinformatics. 17:1228-1229
Cai H, Kumar N, Ai N, Gupta S, Rath P, Baudis M. Progenetix: 12 years of oncogenomic data curation. Nucleic Acids Res (2014) Jan;42
Baudis M. (2006) Online database and bioinformatics toolbox to support data mining in cancer cytogenetics. Biotechniques. 40:296-272.

Registration & Licenses

No specific registration is required for using the refCNV resource. While the data is licensed under CC-BY 4.0 we suggest that you contact Michael Baudis if you plan any commercial use of the database or are interested to incorporate the data into your research projects.

Additional information - e.g. about contacts or related publications - is available through the group page of the Baudis group at the University of Zürich. For a list of publication by the Baudis group you can go to the group's website, EuropePMC or any of the links here.

refCNV Source Code

With exception of some utility scripts and external dependencies (e.g. MongoDB) the following projects provide the vast majority of the software (from database interaction to website) behind Progenetix and Beacon+.

bycon and byconaut

  • Python based service based on the GA4GH Beacon protocol
  • software powering the Progenetix resource
  • Beacon+ implementation(s) use the same code base

refcnv-web

  • website code for the refCNV implementation
  • provides Beacon interfaces for the bycon server, as well as other Progenetix sevices (e.g. the publications repository)
  • implemented as React / Next.js project
  • contains this documentation tree here as mkdocs project, with files in the docs directory