CRI iAtlas
@iatlas-cri.bsky.social
Platform & analytic tools for exploring molecular and cellular response in cancer immunotherapy. Powered by @isbscience.org @sagebio.bsky.social @unclineberger.bsky.social @cancerresearchinst.bsky.social https://cri-iatlas.org/
New data available in CRI iAtlas! iAtlas now includes immunogenomic data derived from the AMADEUS immunotherapy trial. rupress.org/jem/article/... @cancerresearchinst.bsky.social
February 7, 2025 at 5:53 PM
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
December 2, 2024 at 5:55 PM
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
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...
November 26, 2024 at 9:01 PM
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...
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
November 26, 2024 at 9:01 PM
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
New analysis module!📊
Explore the prevalence, variety and distribution of predicted neoantigens in datasets of response to #ImmuneCheckpoint Inhibitors therapy #Immunotherapy #immunogenomics
Explore the prevalence, variety and distribution of predicted neoantigens in datasets of response to #ImmuneCheckpoint Inhibitors therapy #Immunotherapy #immunogenomics
November 26, 2024 at 9:01 PM
New analysis module!📊
Explore the prevalence, variety and distribution of predicted neoantigens in datasets of response to #ImmuneCheckpoint Inhibitors therapy #Immunotherapy #immunogenomics
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
November 26, 2024 at 9:01 PM
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
November 26, 2024 at 9:01 PM
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/
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/
Help - CRI iAtlas
Tutorials
Classify gene expression data in the 6 Immu...
cri-iatlas.org
November 26, 2024 at 9:21 PM
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/
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/
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...
November 26, 2024 at 9:21 PM
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
https://star-protocols.cell.com/protocols/2249
November 26, 2024 at 11:35 PM
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
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
November 26, 2024 at 9:34 PM
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
November 26, 2024 at 9:34 PM
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
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...
November 26, 2024 at 9:34 PM
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
November 26, 2024 at 11:35 PM
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
November 26, 2024 at 9:34 PM
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
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
November 26, 2024 at 11:35 PM
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
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...
November 27, 2024 at 12:12 AM
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.
November 26, 2024 at 10:30 PM
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.
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...
iAtlas Home - CRI iAtlas
CRI iAtlas
The iAtlas portal serves as an interactive to...
cri-iatlas.org
November 26, 2024 at 10:30 PM
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.
November 26, 2024 at 10:30 PM
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
November 26, 2024 at 10:30 PM
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
November 26, 2024 at 10:48 PM
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
November 26, 2024 at 10:48 PM
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
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) http://cri-iatlas.org! 📨
November 26, 2024 at 10:48 PM
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) http://cri-iatlas.org! 📨
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
November 26, 2024 at 11:35 PM
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