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
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
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
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
The IO Targets module at http://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. http://go.nature.com/2RD8KNR #immunoOncology
November 26, 2024 at 11:35 PM
The IO Targets module at http://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. http://go.nature.com/2RD8KNR #immunoOncology
With the new ICI Machine Learning module in http://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
November 26, 2024 at 11:54 PM
With the new ICI Machine Learning module in http://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
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
November 26, 2024 at 11:54 PM
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
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
November 27, 2024 at 12:50 AM
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
To reproduce these plots, you just need to follow these steps:
1. Access our Portal at https://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]
1. Access our Portal at https://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]
November 27, 2024 at 12:33 AM
To reproduce these plots, you just need to follow these steps:
1. Access our Portal at https://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]
1. Access our Portal at https://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]
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 (https://www.nature.com/articles/s41416-020-01145-4)...
November 26, 2024 at 11:54 PM
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 (https://www.nature.com/articles/s41416-020-01145-4)...
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
November 27, 2024 at 12:12 AM
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
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 11:54 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