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 (based on the expression of gene) on the logrank p-value for Kaplan Meier curves with the best survival difference. Next to the KaplanScan option, the R2platform also provides other separation options to assess segregation from gene expression, such as median, quartiles, of the average expression of a gene.

kaplanscan

Create gene set signatures and employ those as meta genes.

Convert lists of genes (gene sets) into a single value and store those as a new meta feature in your account. These meta genes can then be used for association analyses and represent e.g. pathway activities. The R2 platform provides a large resource with public gene set databases such as MSigDB, KEGG pathways and many more. In addition, you can start creating your own gene sets from analyses performed in R2, or by cut and paste in your own account.

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 those with annotations (grouping variables), meta features, gene expression data or other multi omics overlays. You can also define regions of your interest with the lasso tool, or aut-detect clusters using the DBscan algorithm. R2 typically stores multiple embeddings for a data set, from parameter sweeps in UMAP and tSNE settings. These can be helpful in assessing robustness, and finding the optimal view to tell your story.

Single Cell analysis

Precision 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. Simply use one of our public data scopes to see how insightful these representations can be.

Precision 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 chromosome location to integrate the many genome plugins (with adaptable settings) to gain new insights. If you register an account, you can also store these representations as presets for later re-use.

Genome Browser

Epigenome & ChIPseq analyses to explore gene regulation and genome organisation

R2 hosts many public histone modification / transcription factor ChIPseq profiles that can be useful in understanding transcriptional changes. Use the embedded options in the ChIP section such as, TSS plots, multi region views, ROSE super enhancer options and more. In addition, it is also possible to have your private profiles added to R2

Epigenome ChIPseq

R2 citations in NCBI PubMed

The R2 plaform has been cited as a webcite in numerous publications, a listing of which can be accessed from within the platform. These citations also include high impact journals such as Nature and Cell. The author network feature in R2 allows you to see how authors are connected in a playful way.

Genome Browser

Contact us
AUMC, CEMM, 2022