Meta cohort with 28000 bulk gene expression profiles

 Meta cohorts can be very interesting to get a quick comprehensive overview of the gene expression pattern for your gene of interest.

Here a meta cohort that has been around for some time, but still provides valuable information at a single glance. The integration of a harmonised Affymetrix cohort of nearly 28.000 bulk profiles. Using the 'sample maps' feature in the free open online R2 platform ( https://r2.amc.nl ), you can use data driven representations, such as UMAP, tSNE, PCA etc for exploration. Or make use of a wealth of other features available in the versatile data science tool, intended for biomedical researchers.






Comments

Post a Comment

Popular posts from this blog

Plotting updates for the open online R2platform. The data science platform for biomedical researchers

Image
  Ploting updates 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 ...
Read more

R2: An Interactive Online Portal for Tumor Subgroup Gene Expression and Survival Analyses, Intended for Biomedical Researchers

Image
  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...
Read more

Unlocking Insights: Cool Things You Can Do with the Visual Fisher’s Exact Test in R2platform

Image
Unlocking Insights: Cool Things You Can Do with the Visual Fisher’s Exact Test in R2platform The Fisher’s Exact Test is a powerful statistical tool for analyzing categorical data, especially when sample sizes are small. The R2platform ( https://r2platform.com ) takes this classic test to the next level by offering a  visual, interactive interface  (XY-Honeycomb) that makes exploring your data both intuitive and insightful. Here’s a look at all the cool things you can do with the visual Fisher’s Exact Test in R2platform: 1.  Effortless Data Exploration With R2platform’s visual interface, you can quickly analyze a dataset and select the variables you want to analyze. The platform automatically generates an interactive contingency tables equivalent, making it easy to see the distribution of your categories at a glance. 2.  Instant Statistical Testing No need to write code! Simply select your groups, and R2platform runs the Fisher’s Exact Test for you. The results—includ...
Read more