For the seminar on the 19th of October Sinduja Chandrasekaran invited Jan Koster to talk about the R2 tool. If you are interested in joining write an e-Mail to compcancer at charite dot de to receive the zoom link.
R2: Genomics Analysis and Visualization Platform guided by stories from the neuroblastoma research
Overall goal
Development of a dedicated bioinformatics platform, loaded with tools and methods which allow wetlab biologists to interpret their own high-throughput experiments (gene expression data, chip-seq, whole genome sequencing, whole exome, methylation, etc ).
Reaching this goal
R2 is our in house developed web-based bioinformatics analysis and visualization platform that enables analysis of probable targets in the context of (tumor) gene expression data (url: http://r2.amc.nl). Specifically focusing at biologists and biomedical scientists, R2 aids in the analysis and visualization of gene expression data (tumor series, experiments) and their annotated features (such as clinical information). R2 contains an expanding set of analyses which are heavily inter-connected, allowing users to quickly hop from one view (representation of the data) to another. Currently R2 supports all major platforms for human, mouse and rat and harbors more than 1.000.000 public samples (divided over more than 1800 datasets) and in addition also restricted datasets from research groups and consortia. R2 is also being employed in the integration, analysis and visualization of copy numbe / ChIP-seq / Whole genome sequence information in a wide array of research collaborations that include both research groups from around the world, as well as consortia in which we actively participate.