CRI iAtlas: an interactive portal for immuno-oncology research.

F1000Research
James A EddyJustin Guinney

Abstract

The Cancer Research Institute (CRI) iAtlas is an interactive web platform for data exploration and discovery in the context of tumors and their interactions with the immune microenvironment. iAtlas allows researchers to study immune response characterizations and patterns for individual tumor types, tumor subtypes, and immune subtypes. iAtlas supports computation and visualization of correlations and statistics among features related to the tumor microenvironment, cell composition, immune expression signatures, tumor mutation burden, cancer driver mutations, adaptive cell clonality, patient survival, expression of key immunomodulators, and tumor infiltrating lymphocyte (TIL) spatial maps. iAtlas was launched to accompany the release of the TCGA PanCancer Atlas and has since been expanded to include new capabilities such as (1) user-defined loading of sample cohorts, (2) a tool for classifying expression data into immune subtypes, and (3) integration of TIL mapping from digital pathology images. We expect that the CRI iAtlas will accelerate discovery and improve patient outcomes by providing researchers access to standardized immunogenomics data to better understand the tumor immune microenvironment and its impact on patient res...Continue Reading

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Citations

Jun 16, 2021·Journal of Genetics and Genomics = Yi Chuan Xue Bao·Jing YangYu Shyr
Jul 27, 2021·Computational and Structural Biotechnology Journal·Priyanka ChakrabortyJason A Somarelli
Sep 14, 2021·Frontiers in Genetics·David L GibbsIlya Shmulevich

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Methods Mentioned

BETA
RNA-seq

Software Mentioned

dplyr
Zenodo
tibble
IO
tidyverse
R
Synapse
XGBoost
stringr
DataTables

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