We maintain online databases and web-based tools for genome-wide analysis of regulatory regions, gene expression, function, and transcriptional regulation.
Nencki Genomics Database (NGD)
extends the functionality of Ensembl Regulatory Build (funcgen) for the three species: human, mouse and rat. The key enhancements over Ensembl funcgen include the following: (i) a user can add private data, analyze them alongside the public data and manage access rights; (ii) inside the database, we provide efficient procedures for computing intersections between regulatory features and for mapping them to the genes. NGD is a stable mature tool and we encourage its use.
Documentation URL: http://www.nencki-genomics.org
If you use NGD please cite: Krystkowiak et al., Database 2013, PMID: 24089456.
Nencki Expression Webservice (NEWS)
provides functions for analysis of gene expression data: transformation, identification of differential expression, filtering, sorting, merging, subsetting, visualization, clustering and (optionally) intermediate results storage with access rights management. The data are passed between the NEWS functions as a standard XML-based object, permitting chaining of functional operations and unified programmatic access. This is a public beta version, currently undergoing tests.
Documentation URL: http://www.nencki-genomics.org/webservices
Nencki Galaxy Instance
provides graphical user interphase the above resources from a web browser.
Access URL: http://galaxy.nencki-genomics.org/
This is a public alpha version. Please contact us if you would like to try it with our support.