CRI iAtlas

New data available in CRI iAtlas! iAtlas now includes immunogenomic data derived from the AMADEUS immunotherapy trial. rupress.org/jem/article/... @cancerresearchinst.bsky.social

New data available in CRI iAtlas! iAtlas now includes immunogenomic data derived from the PRINCE (pancreatic cancer) and PORTER (prostate cancer) immunotherapy trials. This update also includes data on breast cancer checkpoint treatment from the Human Tumor Atlas @cancerresearchinst.bsky.social

https://github.com/CRI-iAtlas/iatlas-notebooks/blob/main/ici_query_iatlas_data_python.ipynb

New notebook 🚨📒! Python code to access and explore clinical annotation, immune features and gene expression of +1k samples from studies of response to Immune Checkpoint Inhibitors. #Immunotherapy #immunoOncology...

CRI-iAtlas is a collaboration between @isbsci,@Sagebio and the @bgvincentlab of the @UNC_Lineberger. We are thankful to @CancerResearch for supporting this project!

We are excited to share a major milestone in CRI iAtlas: the addition of 2 datasets with single-cell RNA-seq and analysis modules! #immunoOncology #singlecell #RNAseq

Neoantigen prediction was performed by the @bgvincentlab, using the Landscape of Effective Neoantigens Software (LENS) workflow https://academic.oup.com/bioinformatics/article/39/6/btad322/7162685

New analysis module!📊

Explore the prevalence, variety and distribution of predicted neoantigens in datasets of response to #ImmuneCheckpoint Inhibitors therapy #Immunotherapy #immunogenomics

Our platform allows you to select a cohort: you select dataset(s) of interest, add filters, and select how samples should be grouped. The visualizations will adapt to your selection and you will be able to explore your selected cohorts! #immunoGenomics

We have a collection of tutorials describing steps to common analysis in iAtlas. In one of them, you can learn how to create your custom cohort of TCGA, PCAWG or Immune Checkpoint Inhibitors datasets. Check it out at https://cri-iatlas.org/help/ 📒📖 #tutorial #ImmunoOncology

How do I cite CRI iAtlas? Can I add my own data to visualizations in CRI iAtlas?

These are some of the questions that we included in the FAQ in our Help page! Check it out at: https://cri-iatlas.org/help/

https://github.com/CRI-iAtlas/iatlas-notebooks/blob/main/querying_TCGA_features_and_expression.ipynb

Check out our newest notebook! Get an overview on how to query the CRI iAtlas to get clinical data, immune features, and quantile normalized gene expression for TCGA. #cancerGenomics #JupyterNotebook...

The STAR Protocols publication on "Analytic pipelines to assess the relationship between immune response and germline genetics in human tumors" has been published 🥳
https://star-protocols.cell.com/protocols/2249

Our Hazard Ratio module was designed to compare Cox proportional hazard ratio of immune features across the 12 Immune Checkpoint Inhibition (ICI) datasets in CRI iAtlas. #cancerGenomics #immunoOncology

The CRI iAtlas Immune Features module displays the distribution of immune readouts across your selected groups. In the image, we can see the estimates of T Cells CD4 for 5 datasets, with samples grouped based on the response to #ImmuneCheckpoint Inhibitor therapy. #immunotherapy

(https://github.com/CRI-iAtlas/iatlas-notebooks/blob/main/ici_query_iatlas_data.ipynb) #immunoOncology

Do you want to explore the data from studies of response to Immune Checkpoint Inhibitors (ICI) available in iAtlas? Check out the ICI Dataset Overview module (https://isb-cgc.shinyapps.io/iatlas/?module=ioresponse_overview) in our web app and our notebook...

The CRI iAtlas notebooks allow you to reproduce visualizations available at our portal, and can also be used to add your own data in the analysis. #immunoOncology #CancerResearch

Data update! Explore immune analysis of 1351 samples, across 15 datasets, from studies of response to Immune Checkpoint Inhibitors (ICI) at http://cri-iatlas.org. #immunoOncology #CancerResearch

The Germline Analysis module is based on the manuscript by Sayaman, @MohSaad2012 et al, co-led by @ziv_elad and @DBedognetti published @ImmunityCP @UCSF @UCSFCancer, @QatarComputing, @SidraMedicine https://www.cell.com/immunity/fulltext/S1074-7613(21)00034-0

#immunoOncology #machineLearning

Do you want to use the Immune Checkpoint Inhibitors data to build your own model?Or maybe you want to include your own data? We have notebooks laying out the steps to query the iAtlas data and use the result to build models https://github.com/CRI-iAtlas/iatlas-notebooks...

Compare #geneExpression values with our Immunomodulators module. Select datasets, add filters, and select how to group samples. The immunomodulators module provides plots with distribution of values of expression of a selected gene with statistics comparing the selected groups.

over selected sample groups.

You can explore in http://cri-iatlas.org the results of the analysis of #TCGA digital pathology images for tumor infiltrating lymphocytes (TILs) (described at https://www.cell.com/cell-reports/fulltext/S2211-1247(18)30447-9): select a TIL map characteristic to see its distribution...

Explore driver genes and oncogenic mutations associated with #immuneFeatures in http://cri-iatlas.org. The figure below displays a volcano plot with the degree of association between driver mutations and Leukocyte Fraction readouts across all tumors characterized by the #TCGA.

Explore predicted extracellular networks modulating tumoral immune response. In the figure below,the subnetwork centered on CD8 T cells shows ligands and receptors abundantly expressed and edges with both nodes frequent and simultaneously highly or lowly expressed #immunogenomics

Explore in http://cri-iatlas.org the germline genetic contribution to the immune landscape of cancer with results of heritability analysis, GWAS, and rare variant analysis across 30 cancer types characterized by the TCGA #immunoOncology #cancerGenomics

Explore the immune cell proportions in #cancerGenomics datasets in http://cri-iatlas.org. In the image, immune cell estimates for #TCGA samples grouped by immune subtype are plotted in a barplot. #immunoOncology #dataVisualization