R2 Genomics Analysis and Visualization Platform

Welcome to R2, an online datamining and discovery platform designed to assist the bio-medical researchers with limited to no Bioinformatics skills to perform datascience tasks in the omics field.

The R2 platform has completely been built in the academic medical center in Amsterdam, the Netherlands by the team of Dr. Koster (Formerly in the Department of Oncogenomics, since 2021 within the Center for Experimental and Molecular Medicine (CEMM)).

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Differential Expression Analyses in an interactive fashion without scripting.

The interface and design of R2 has been created to easily follow your path by inter connecting analyses and data visualization there of. This allows you to follow an hypothesis from a bird's eye view up to the details of a statistical test result and vice versa.

Interactive Differential Expression

Perform Survival Analyses on Gene Expression with Optimal Cutoffs

Use our KaplanScanner tool to find the optimal 2 group segregation on the logrank pvalue for kaplan Meier curves with the best survival difference

kaplanscan

Create gene set signatures and employ those as meta genes.

Convert lists of genes into a single value and store those as a new feature in your account. These meta genes can then be used for association analyses and represent e.g. pathway activities.

Gene set signatures

Single Cell RNA-seq Exploration

Generate new embeddings or explore (published) dimensionality reduction views (PCA, tSNE, UMAP) of single cell experiments. Overlay meta features, gene expression data or other multi omics overlays.

Single Cell analysis

Personalized Medicine Platform multi omics integration for single patient data

Use our different entry points (e.g. onco plot, circos views, mutation view etc. ) to assess targets for potential treatment options from the R2 integrated single sample overviews. These features are also insightful for (PDX / Cell line) model systems.

Pers. Medicine

Use our Embedded Genome Browser completely integrated with the R2 Tools

Use our embedded genome browser to change perspective on your differential expression analyses, or simply use the chomomosome location to integrate the many genome plugins to gain new insights.

Genome Browser

Epigenome & ChIPseq analyses to explore gene regulation and genome organisation

Re hosts many public histone modification / transcription factor ChIPseq profiles that can be useful in understanding transcriptional changes. In addition, it is also possible to have your private profiles added to R2.

Epigenome ChIPseq

Contact us
AUMC, CEMM, 2022