Releases: CRI-iAtlas/iatlas-app
Releases · CRI-iAtlas/iatlas-app
2.4.1
Release of the iAtlas App version 2.4.1!
New data:
Added bulk RNA-seq data datasets with characterization of response to Immune Checkpoint Inhibitor: for the AMADEUS trial (2024)
Updates:
Bug fixes
Full Changelog: 2.4...2.4.1
2.4
Release of the iAtlas App version 2.4!
New Data
- PRINCE trial (2022)
- PORTER trial (2022)
- Johnson et al., Cell Reports Medicine, 2022 (This data set was generated as part of the NCI Human Tumor Atlas Network, shared via https://humantumoratlas.org/)
New functionality
-
Single Cell Cohort Selection. Data for the single cell datasets can now be selected in the Single Cell Cohort Selection, with options of filters and groups.
-
Bug fixes.
Full Changelog: 2.3.1...2.4
2.3.1
New data:
Added 4 single-cell RNA-seq datasets:
- Bi et al. Cancer Cell, 2021
- Li et al. Cancer Cell, 2022
- Krishna et al. Cancer Cell, 2021
- Shiao et al. Cancer Cell, 2024
Updates:
- Data for pseudobulk single-cell datasets retrieved by API calls
- Bug fixes
2.3
New data:
- Added two single-cell RNA-seq datasets:Chan et al. Cancer Cell, 2021, Chen et al. Cell, 2021. These data sets were generated as part of the NCI Human Tumor Atlas Network, shared via https://humantumoratlas.org/
New modules:
- UMAP: Explore UMAP plots of single-cell RNA-seq datasets.
- Immune Features: See how immune readouts in pseudobulk single cell RNA seq datasets.
- Immunomodulators: Explore the expression of genes that code for immunomodulating proteins, including checkpoint proteins in pseudobulk single cell RNA seq datasets.
Updates:
- Datasets Overview page now provides information about all datasets available in CRI iAtlas.
2.2
New data:
- Added neoantigen data for 5 datasets: Hugo et al. Cell, 2016, McDermott et al. Nature Medicine, 2018 (IMmotion150), Kim et al. Nature Medicine, 2018, Liu et al. Nature Medicine. 2019, e Van Allen et al. Science, 2015. Neoantigen prediction was performed using the Landscape of Effective Neoantigens Software (LENS) workflow (Vensko 2023)
New module:
- ICI Neoantigen: Explore the prevalence, variety and distribution of predicted neoantigens in datasets from studies of Immune Checkpoint Inhibitors therapy
Updates:
- Added links to tutorials and/or Jupyter Notebooks for the Immune Subtype Classifier tool, and the ICI Machine Learning, ICI Hazard Ratio, Clinical Outcomes, Tumor Microenvironment, and Immune Features modules
- Added links in ICI Cohort Selection and CG Cohort Selection to notebooks that describe how to query the CRI iAtlas database
- ICI Hazard Ratio module now accepts the selection of gene expression data
- Bug fixes
2.1.2
2.1.1
2.1
- Added 4 Nanostring datasets from studies of Immune Checkpoint Inhibitors therapy. The new data can be explored in the Immunomodulators module
- Updated app color scheme
- Resources and About pages now redirect to corresponding pages in cri-iatlas.org
- Notebooks page now redirects users to the corresponding Github repository
- Updated R to version 4.2.
- Bug fixes
2.0
New data:
- Added PCAWG
- Added 6 datasets from studies of Immune Checkpoint Inhibitors therapy
New modules:
- ICI Cohort Selection and CG Cohort Selection: Select dataset of interest and then add grouping and numeric filters. These selections can then be compared and contrasted using a variety of grouping variables, such as driver mutations.
- ICI Machine Learning: Train and run multivariable models with cross-validation on ICI genomics and immunogenomics data.
Updates:
- Updated GWAS data in Germline Analysis module: GWAS results are now displayed in an IGV plot
- iAtlas data is now stored in a PostgreSQL database and is retrieved dynamically through a GraphQL API