R2platform datascience annals

Genomic data from The Cancer Genome Atlas (TCGA) project has enabled comprehensive molecular profiling of diverse cancer types. The extensive sample size within TCGA provides an invaluable resource for investigating tumor heterogeneity. Effective exploration of this dataset by researchers and clinicians is essential for discovering novel therapeutic and diagnostic biomarkers.  The R2Platform, provides an easy interface to explore the rich resource at different levels. By example, subset the cohort to paired tumor / normal patients only and discover how the expression of your gene of interest changes from normal to tumor. The R2 data science platform for biomedical researchers serves as a robust tool for in silico validation of target genes and the identification of candidate biomarkers for tumor subtype-specific research. The R2 portal has the potential to accelerate cancer research by providing accessible and comprehensive analytical capabilities. R2 is already cited in more than ...

  R2: An Interactive Online Portal for Tumor Subgroup Gene Expression and Survival Analyses, Intended for Biomedical Researchers Genomic data from The Cancer Genome Atlas (TCGA) project has enabled comprehensive molecular profiling of diverse cancer types. The extensive sample size within TCGA provides an invaluable resource for investigating tumor heterogeneity. Effective exploration of this dataset by researchers and clinicians is essential for discovering novel therapeutic and diagnostic biomarkers. While numerous computational tools have been developed to analyze specific aspects of TCGA data, there remains a need for platforms that facilitate the study of gene expression variability and its association with clinical outcomes across tumors. Here, we introduce the  R2 Platform , an intuitive and interactive web portal designed for in-depth analysis of TCGA gene expression data. The portal leverages TCGA Level 3 RNA-seq and clinical data from 31 cancer types. With its user-f...

The definition of genes and transcripts contained within these bounderies is by no means fixed. As a scientific community we keep on learning, resolving and discovering adaptations on our gene models. The Gencodegenes consortium forms a rich resource that keeps us up to speed with the recent developments in our understanding and composition of transcripts. They do this with version controlled updates that occur a few times per year. Within the embedded Genome Browser of the R2 genomics analysis and visualization platform ( https://r2.amc.nl ), we also maintain a Gencode version Time Machine track. This track allows you to easily grasp how some transcripts are very stable, and have not changed at all, while others are still changing from gencode version to version. Within R2 we also publicly provide the RNA Atlas, which is a comprehensive collection of deeply profiled ~300 tissues, cell types and cancer cell lines, all assessed by polyA as well as total RNA sequencing. This rich resou...

The open online genomics platform R2, has been cited in NCBI Pubmed listed schientific literature for a stunning 2597 times to data. These citations cover the whole range in terms of impact factors and include some seminal papers, published in Nature, Cell and comparable journals. Please visit the citation-list within R2 to have a look, or even better Try the R2platform with your own genomics type questions and simply see how far you can get by re-use of publicly available resources. R2 already hosts more than 2,400 different data sets (resources) in the public space alone. These include frequently used sets such as TCGA, GTEx, DepMap and thousands of other cohorts / panels / experiments. Interested? Visit  https://r2.amc.nl  and discover something new Today

  Plot update for the R2platform We have been working hard to bring you the latest update in the R2 genomics analysis and visualization platform ( https://r2.amc.nl ); the goto web-tool for biomedical researchers to test their hypotheses on public omics data, without the need for bioinformatics or coding expertise. In the latest update, we have made substantial changes to many of the plots that can be produced within R2. Many of the adaptable parameters have now become interactive and are placed under the 'gears' icon. The 'gears' icon Let's have a look at a gene within one of the many resources that are publicly available in R2. We will look at the GATA3 gene in an integrated resouce where samples from both GTEx as well as the TCGA have been integrated and 'batch corrected' to get an immersive view of expression in normal as well as cancer samples. We first select our resource of interest by clicking on 'select a data set'. and then find the 'TC...

The R2 platform has been celebrating quite some achievements that we have never even considered when we started developeing the R2 platform. Some weeks ago, we reported on 2.500 citations for the R2 platform in NCBI PubMed. This was already a dream come through. Now we can report on yet another milestone. We have been visited by 250.000 unique IP addresses in the R2 platform. A major achievement that would not have been possible without the many users that serve as true ambassadors by spreading the word on the usefulness of the platform, especially for scientists that are not able to easily download, pre-process and subsequently analyse genomics data. And why should they, is they can also just visit R2 and click your way through a wide array of analytical options.   So spend your time thinking about the results, in stead of preparing the data.