R2platform Data Science Annals

Create a visual Fisher's Exact plot in a few simple clicks in the R2 Genomics Analysis & Visualization platform ( https://r2.amc.nl ). Just see the whole process in action in the illustration below. The Fisher's Exact test is often used to demonstrate whether the proportions of 2 different categorical variables are equal to the expectation. A significant p-value then informs you that this is unlikely (when used as a 2-sided test). Within R2, we add a visual element to such a test, where you can see the different groups in the contingency table as separate dots. These dots, are linked to actual samples in the data set, and can thus also be decorated using their meta data (color by a grouping variable), or even by the expression of any gene. As such you can add another layer in your interpretation. Just have a look at the animation above on how you can easily use this powerful option within the R2platform. The R2 open access online data science platform, designed for biomedic...

Create a stacked bar plot in a few simple clicks in the R2 Genomics Analysis & Visualization platform (https://r2.amc.nl). Just see the whole process in action in the illustration below. The R2 open access online data science platform, designed for biomedical researchers, has more than 2,600 public resources (totalling >4,000,000 samples combined) available for instant analysis. Academic usage of R2 is free, so direct your browser to https://r2.amc.nl and start exploring TCGA, DepMap, GTeX or one of the other 2,600 resources.

Explore data-driven embeddings, such as UMAP, tSNE etc on more than 2500 public resources in the 'sample maps' tool of the R2 platform. This is just one of the many avenues R2 has to offer for scientists who are not experts in bioinformatics or coding. R2: open online data science platform for biomedical researchers ( https://r2.amc.nl )

Cancer is often considered a disease of the genome, where changes in the DNA accumulate, due to selective advantages that they may confer. These changes can be large, termed chromosomal abberations, or very small (affecting 1 or more bases), called small nucleotide variations. Chromosomal abberations in Cancer come in 6 different flavours Small nucleotide variations in Cancer come in 3 different flavours 

The Cancer Genome Atlas Program (TCGA) is one of the cornerstones of cancer research. Every sample has a unique identifier, also known as barcode. A basic understanding of the naming convention is very helpful to quickly assess the 'type of sample' that you are working with. The sample type is contained in the numerical part of the 4th element of a barcode, that can be up to 7 parts. Barcodes most commonly are composed of 4 parts, which is informative for most use cases. Code Definition 1 Primary Solid Tumor 2 Recurrent Solid Tumor 3 Primary Blood Derived Cancer - Peripheral Blood 4 Recurrent Blood Derived Cancer - Bone Marrow 5 Additional - New Primary 6 Metastatic 7 Additional Metastatic 8 Human Tumor Original Cells 9 Primary Blood Derived Cancer - Bone Marrow 10 Blood Derived Normal 11 Solid Tissue Normal 12 Buccal Cell Normal 13 EBV Immortalized Normal 14 Bone Marrow Normal 15 sample type 15 16 sample type 16 20 Control Analyte 40 Recur...

  Relate the expression of any gene to survival potential using the embedded tools available in the R2 open online datascience tool  (  https://r2.amc.nl  ) . Scan for genes with potential using Cox proportional hazard analysis, and explore those in more details, using the interactive visualization tools. Or alternatively find genes with the optimal logrank separation and view those in interactive Kaplan Meier plots. With the identified cut-off(s), you can easily create a new grouping variable and use those to perform in depth analyses, such as differential expression within a few click of the mouse. Any gene of interest can also be validated in numerous other resources that are publicly available as well (n>2500 resources). All this and much much,more is available in the free open online R2 platform (  https://r2.amc.nl  ).