Help

Help2024-04-09T13:14:19-08:00

Tutorials

  • Classify gene expression data in the 6 Immune Subtypes described by Thorsson et al, 2018 (Tutorial)
  • Create a Cohort in iAtlas (Tutorial)
  • Compare outcome data in Immune Checkpoint Inhibition datasets using Cox proportional hazard models (Tutorial)
  • Create a Machine Learning model using the data on Response to Immune Checkpoint Inhibitors (Tutorial)
  • Explore neoantigen data in CRI-iAtlas (Tutorial)

FAQ

What is CRI iAtlas?2022-09-14T09:26:30-08:00

The Cancer Research Institute (CRI) iAtlas is an interactive web platform and a set of analytic tools for studying interactions between tumors and the immune microenvironment.

Who maintains this portal?2022-09-14T09:51:41-08:00

CRI iAtlas is made possible through a collaboration between the Cancer Research Institute, Sage Bionetworks, the Institute for Systems Biology, and the Vincent Lab at the UNC Lineberger Comprehensive Cancer Center.

How do I cite CRI iAtlas?2022-09-14T09:56:25-08:00

Please cite the CRI iAtlas paper (PubMed: 33214875) when you use CRI iAtlas.

Eddy JA, Thorsson V, Lamb AE, Gibbs DL, Heimann C, Yu JX, Chung V, Chae Y, Dang K, Vincent BG, Shmulevich I, Guinney J. CRI iAtlas: an interactive portal for immuno-oncology research. F1000Research 2020, 9:1028.

How can I contact the team with questions?2022-11-22T06:07:51-08:00

Please send us a message to support@cri-iatlas.org. Also consider opening a Github issue in the app repository.

Are there CRI iAtlas resources beyond the web app?2022-09-14T09:42:47-08:00

Yes!

The code for the CRI iAtlas web app is open source and available at our Github repository .

We also have a collection of notebooks that you can run to carry out functionality made available by the iAtlas platform, as well as how carry out additional functions, such as enabling the integration of your data with what’s already in iAtlas.

You can access our workflows in Dockstore.

Can I contribute to CRI iAtlas?2022-10-06T08:38:02-08:00

Yes! If you would like to contribute code changes please follow these steps:

  1. Search the issues list in the repo. Consider opening an issue related to the suggested feature.
  2. For new code development, create a personal fork and commit new code in that fork.
  3. Propose changes via pull request of personal branches.

If you want to contribute data to iAtlas, please contact us.

Can I add my own data to visualizations in CRI iAtlas?2022-09-27T08:53:54-08:00

We have a collection of notebooks that you can run to carry out functionality made available by the iAtlas platforms, which enables the integration of your data with what’s already in iAtlas.

How can I learn more about the data in CRI iAtlas?2022-09-27T08:54:01-08:00

You can learn more about Cancer Genomics datasets available in CRI iAtlas in their original sources: TCGA and PCAWG.

You can learn more about the Immune Checkpoint Inhibition datasets in the Datasets Overview module.

How does the CRI iAtlas classifier work?2022-10-06T08:36:25-08:00

The method to classify Immune Subtypes is described at Robust classification of Immune Subtypes in Cancer | bioRxiv.

Which methods were used to obtain variables?2022-10-06T08:35:01-08:00

A description of variables and methods is available in the Data Description section of the CRi iAtlas web app.

Can I download all the data?2022-10-06T08:35:26-08:00

Yes! You can download the data in CRI iAtlas from Synapse.

Can I use images from CRI iAtlas in my publication?2022-10-06T08:35:56-08:00

Yes! Please cite the CRI iAtlas paper (PubMed: 33214875) when you use CRI iAtlas.

Eddy JA, Thorsson V, Lamb AE, Gibbs DL, Heimann C, Yu JX, Chung V, Chae Y, Dang K, Vincent BG, Shmulevich I, Guinney J. CRI iAtlas: an interactive portal for immuno-oncology research. F1000Research 2020, 9:1028.

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