Rep-seq Playground is currently available for beta testing for a limited number of users. Please contact us if you are interested to participate in our beta program.
Rep-seq Playground will be our next-generation interactive visualization platform for immune repertoire analysis in immunomics and immuno-oncology.
Analyze your immunological data easily, quickly and in-depth with RepSeq Playground. Discover the impressive features and tools you can find in the platform and how easy to use they are, making sophisticated analysis more accessible to biologists.
By entering the RepSeq Playground, you will find a first tab called “Statistics”. Here, you will be able to visualize your data both in the shape of a pie and a bar chart, and decide whether you want to see the percentages or the numbers. You can also decide whether you want to visualize Heavy, Kappa or Lambda sequences. Specifically, for the bar chart analysis you can decide whether you want to see the length distribution of CDR1, CDR2 or CDR3.
VJ usage and isotype distribution
Additionally, you can visualize the gene usage in a bar or a line chart where you have the possibility to see the differences between Heavy, Kappa and Lambda chains, and how each of these chains relates to the V and J genes. In addition to that, you can visualize the isotype distribution of the experiments in the shape of a heatmap or a line chart. All these charts and tables allow you to easily visualize the different experiments together, getting some quick insights on your datasets before moving on to a more in-depth analysis.
Clone explorer: Visualisation and Analytics of Clonal families
Have some fun analyzing the clonal families interactively. You can decide how to colour the clones based on several factors and filter by them. By clicking on one clonal family you will be able to see how the different cells relate to each other and, by moving your mouse on the cells, you can discover several information about each of them. Additionally, you can visualize the clonal relationships between cells by moving the mouse on the colored links and, based on the color, you will know if the Heavy, Lambda or Kappa chain exceeds the thresholds.
Phylo explorer: Interactive phylogenetic tree visualization
You can select the algorithms in the subtabs to compare their trees. Five different phylogeny algorithms have been implemented: PHYLIP: DNAML; PHYLIP: PROML; APE:NJ; APE:BIONJ; and MST. Zoom in if the labels are invisible, since the trees are interactive. Edge labels show the nucleotide difference in two sequences for all the algorithms except PHYLIP:PROML (for this algorithm edge labels show amino acid difference).
HSEQ, KSEQ, AND LSEQ explorers: Multiple Sequence Alignment
Here you can analyze each chain, Heavy, Kappa and Lambda, more in detail. You can select the type of sequence (amino acid AA or nucleotide NT) to be displayed in the Hseq, Kseq, and Lseq alignment tabs. Scroll right/left & top/bottom on the alignment to see the complete view. In addition, it is possible to highlight the sequence by clicking on the label, and hide it in the “Filter” subtab. Go to the Selection subtab to invert the selected sequences.