iiinova — where your digital self keeps evolving

CRI iAtlas @iatlas-cri.bsky.social · 07/02/2025

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

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CRI iAtlas @iatlas-cri.bsky.social · 02/12/2024

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

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CRI iAtlas @iatlas-cri.bsky.social · 02/07/2024

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...

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CRI iAtlas @iatlas-cri.bsky.social · 28/03/2024

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

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CRI iAtlas @iatlas-cri.bsky.social · 28/03/2024

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

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CRI iAtlas @iatlas-cri.bsky.social · 20/12/2023

Neoantigen prediction was performed by the @bgvincentlab, using the Landscape of Effective Neoantigens Software (LENS) workflow academic.oup.com/bioinformatics/art…

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CRI iAtlas @iatlas-cri.bsky.social · 20/12/2023

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

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CRI iAtlas @iatlas-cri.bsky.social · 02/08/2023

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

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CRI iAtlas @iatlas-cri.bsky.social · 05/07/2023

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 cri-iatlas.org/help 📒📖 #tutorial #ImmunoOncology

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CRI iAtlas @iatlas-cri.bsky.social · 22/03/2023

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: cri-iatlas.org/help

cri-iatlas.org

Help - CRI iAtlas

Tutorials Classify gene expression data in the 6 Immu...

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CRI iAtlas @iatlas-cri.bsky.social · 26/01/2023

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...

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CRI iAtlas @iatlas-cri.bsky.social · 05/01/2023

The STAR Protocols publication on "Analytic pipelines to assess the relationship between immune response and germline genetics in human tumors" has been published 🥳 star-protocols.cell.com/protocols/2…

star-protocols.cell.com

Cell Press: STAR Protocols

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CRI iAtlas @iatlas-cri.bsky.social · 25/10/2022

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

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CRI iAtlas @iatlas-cri.bsky.social · 17/10/2022

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

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CRI iAtlas @iatlas-cri.bsky.social · 29/09/2022

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 (isb-cgc.shinyapps.io/iatlas/?module…) in our web app and our notebook...

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CRI iAtlas @iatlas-cri.bsky.social · 12/09/2022

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

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CRI iAtlas @iatlas-cri.bsky.social · 06/09/2022

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

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CRI iAtlas @iatlas-cri.bsky.social · 09/08/2022

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 github.com/CRI-iAtlas/iatlas-notebo…...

github.com

GitHub - CRI-iAtlas/iatlas-notebooks: Collection of R not...

Collection of R notebooks to enable local iAtlas plotting...

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CRI iAtlas @iatlas-cri.bsky.social · 01/08/2022

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.

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CRI iAtlas @iatlas-cri.bsky.social · 26/07/2022

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

cri-iatlas.org

iAtlas Home - CRI iAtlas

CRI iAtlas The iAtlas portal serves as an interactive to...

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CRI iAtlas @iatlas-cri.bsky.social · 20/07/2022

Explore driver genes and oncogenic mutations associated with #immuneFeatures in 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.

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CRI iAtlas @iatlas-cri.bsky.social · 11/07/2022

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

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CRI iAtlas @iatlas-cri.bsky.social · 28/06/2022

Explore in 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

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CRI iAtlas @iatlas-cri.bsky.social · 21/06/2022

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

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CRI iAtlas @iatlas-cri.bsky.social · 13/06/2022

Do you think CRI iAtlas can help you explore a specific #immunoOncology question, but are unsure on how to explore our platform to get this information? Send us a direct message or email us at support (at) cri-iatlas.org! 📨

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CRI iAtlas @iatlas-cri.bsky.social · 08/06/2022

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CRI iAtlas @iatlas-cri.bsky.social · 31/05/2022

The IO Targets module at cri-iatlas.org allows you to explore the expression (in tumors) of the extended list of targets of IO therapy compiled by the @CancerResearch Clinical Accelerator team. go.nature.com/2RD8KNR #immunoOncology

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CRI iAtlas @iatlas-cri.bsky.social · 25/05/2022

With the new ICI Machine Learning module in cri-iatlas.org, you can, *on your web browser*, train and run multivariable models with cross-validation on genomics and immunogenomics data from studies of response to Immune Checkpoint Inhibitors. #immunoOncology #rShiny

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CRI iAtlas @iatlas-cri.bsky.social · 17/05/2022

You can compare the abundance of immune cells, ligands and receptors across different groups in an illustration with the CRI iAtlas Cell-Interaction Diagram. In the image below, we can compare two subtypes of SKCM in TCGA samples. #cancerGenomics #immunoOncology #rShiny

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CRI iAtlas @iatlas-cri.bsky.social · 09/05/2022

3. Go to Clinical Outcomes. You can also select the survival endpoint and whether to include confidence intervals and a risk table! [3/3] #cancerGenomics #immunoOncology #rShiny

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CRI iAtlas @iatlas-cri.bsky.social · 09/05/2022

To reproduce these plots, you just need to follow these steps: 1. Access our Portal at cri-iatlas.org 2. Go to ICI Cohort Selection, and then select the ICI datasets of interest (here we selected the two datasets in the previous tweet) [2/3]

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CRI iAtlas @iatlas-cri.bsky.social · 09/05/2022

Plot survival curves based on immune characteristics in our Clinical Outcomes Modules. In the image below, we can compare KM plots for two immune checkpoint inhibitor datasets, with patients stratified based on their MIRACLE Score (www.nature.com/articles/s41416-020-…)...

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CRI iAtlas @iatlas-cri.bsky.social · 25/04/2022

For example, this plot shows the univariable Cox proportional results of three potential markers of response to treatment with ICI as predictors of time to survival endpoint for 5 studies of ICI in Skin Cutaneous Melanoma (SKCM). #immunotherapy

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CRI iAtlas @iatlas-cri.bsky.social · 25/04/2022

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CRI iAtlas @iatlas-cri.bsky.social · 29/03/2022

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.📈 github.com/CRI-iAtlas/iatlas-notebo… #immunology #immunogenomics

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CRI iAtlas @iatlas-cri.bsky.social · 23/03/2022

Our recent release includes the ability to select cohorts for analysis! You can select a dataset of interest and add grouping and numeric filters. These selections can then be compared and contrasted using a variety of grouping variables, such as driver mutations #immunoGenomics

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CRI iAtlas @iatlas-cri.bsky.social · 17/03/2022

Do you want to use 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 to build models with it at github.com/CRI-iAtlas/iatlas-notebo… #immunoOncology...

github.com

GitHub - CRI-iAtlas/iatlas-notebooks: Collection of R not...

Collection of R notebooks to enable local iAtlas plotting...

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CRI iAtlas @iatlas-cri.bsky.social · 14/03/2022

Check out our collection of R notebooks at github.com/CRI-iAtlas/iatlas-notebo…. Each notebook focuses on a specific analysis and enables the local integration of your data with what's already in iAtlas. @CancerResearch @isbsci @Sagebio #immunoOncology

github.com

GitHub - CRI-iAtlas/iatlas-notebooks: Collection of R not...

Collection of R notebooks to enable local iAtlas plotting...

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CRI iAtlas @iatlas-cri.bsky.social · 10/03/2022

Explore immune analysis of 1142 samples, across 12 datasets, from studies of response to Immune Checkpoint Inhibitors (ICI) at cri-iatlas.org. Big thanks to our collaborators @bgvincentlab of the @UNC_Lineberger for all the work in processing and harmonizing these data!

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CRI iAtlas @iatlas-cri.bsky.social · 09/03/2022

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CRI iAtlas @iatlas-cri.bsky.social · 08/03/2022

CRI iAtlas now includes analysis of immune response in tumor samples from PCAWG dcc.icgc.org/pcawg. We are thankful to @OICR_news for the help in adding this data to our platform! #immunoOncology @CancerResearch @isbsci @Sagebio

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CRI iAtlas @iatlas-cri.bsky.social · 07/03/2022

We 🤩our new landing page 🔗http://cri-iatlas.org! The amazing @Allisonx worked with us to revamp our homepage. The hero banner is her and @jamesaeddy’s artwork from the Immune Landscape of Cancer paper, which was the original inspiration for CRI iAtlas 💡

cri-iatlas.org

iAtlas Home - CRI iAtlas

CRI iAtlas The iAtlas portal serves as an interactive to...

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