R2platform Data Science Annals

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  ).

The RNA atlas that is hosted in the R2 Platform ( https://r2.amc.nl ) is a great 300 samples reseource where all of the samples have been analysed on polyA isolation, ribo depletion as well as small RNA sequencing. As such it is an invaluable resource that can also be used to investigate the effects of the different isolation methods. You can use the 'two-set view' to analyze andvisualize 2 resources head-to-head h For example check out the expression of a Histone gene (that lacks a poly A tail), where you can clearly see that the poly A isolation lacks the aility to assess the expression of such genes.  Or visualize the profiles in the landscape views in the embedded genome browser of R2. Just a couple of simple things that R2 can be of great value with a few mouse clicks. Visit  https://r2.amc.nl  and explore this, or one of the hundreds of other public resources from the comfort of your web browser