v1.5.1

Updates:

• Updated GWAS data in Germline Analysis module: now a selection of a SNP will create a link to the corresponding selection in Pheweb.
• Added list of manuscripts in Resources section.

v1.5.0

New Module:

• Added Germline Analysis Module: This module provides interactive visualizations related to the manuscript Sayaman et al., Germline genetic contribution to the immune landscape of cancer, Immunity (2021), https://doi.org/10.1016/j.immuni.2021.01.011
  Explore the germline genetic contribution to the immune landscape of cancer with results of heritability analysis, GWAS, and rare variant analysis across 30 non-hematological cancer types characterized by the TCGA.

v1.4.1

Updates:

• A “How to Cite Us” section in the About page.
• Ability to download gene expression values for all genes in the Immune Checkpoint Inhibitors (ICI) dataset.
• IO dataset files added that were needed for version 1.4. (see issue #208).

v1.4.0

New Modules

• Added Immune Checkpoint Inhibitors modules: The ICI Modules provide visualization of datasets from studies of treatments with Immune Checkpoint Inhibitors (ICI):

  • ICI Datasets Overview: Explore categories and groups of the available datasets.

  • ICI Immune Features: See how immune readouts vary across your groups and ICI datasets.

  • ICI Clinical Outcomes: Plot survival curves based on immune characteristics and identify variables associated with outcome.

  • ICI Hazard Ratio: Create Cox Proportional Hazard Regression Models and visualize Hazard Ratio in a heatmap and a forest plot.

  • ICI Immunomodulators: Explore the expression of genes that code for immunomodulating proteins, including checkpoint proteins.

v1.3.1

Analysis modules updates:

• Violin plots and boxplots can be ordered based on median, max, min values.
• Groups in the barplots at the Tumor Microenvironment Module can be ordered based on the min, max, or mean value of a variable.
• Networks in the Extracellular Network module now have edge widths proportional to the concordance score.
• IO Targets module includes new targets described in Immuno-oncology drug development forges on despite COVID-19 by Samik Upadhaya, Vanessa M. Hubbard-Lucey and Jia Xin Yu; Nature Reviews Drug Discovery, 18 Sep 2020.

Tool update:

• Immune-subtype classifier has a new interface to download the Subtype Classification table.
• Addition of interface to download list of genes used for classification.

v1.3.0

New Modules

• Added Cytokine Network module: Explore the extracellular networks modulating tumoral immune response, encompassing direct interaction among cells and communication via soluble proteins such as cytokines to mediate interactions among those cells.
• Added Copy-number Correlation module: Explore statistical associations between immune readouts and gene-level copy number variations.
• Added Cell-interaction Diagram module: This module allows you to depict the estimated abundance of tumor cells and representative innate and adaptive cells in the microenvironment, along with the abundance of receptor and ligands mediating interactions between those cells.

New Documentation

• Added Contributing Guide for pointers on how to get started on a new module.

v1.2.0

• New module IO Targets made available
• More robust classifier included in immune subtype classification tool, using a new R package
• Additional data splitting choices provided in outcome module
• Plot interactivity enhanced using plotly capabilities
• Distribution plots now available as either box or violin plots
• Variable scaling available in distribution plots
• Additional choices of correlation metrics for plots made available
• Details of sample group annotations now visible by clicking on plot tick-labels
• Moving of code from module files into testable functions
• Improved build structure, using the R renv package
• Improved installation instructions in README

v1.1.0

General refactoring and cleanup of code, aesthetics. New features include:

• Two new analysis modules:
  • TIL Maps — Explore the characteristics of maps of tumor infiltrating lymphocytes obtained from analysis of H&E images
  • Driver Associations — Explore associations of microenvironment with driver mutations
• Option in Sample Groups Overview module to upload and use custom sample group definitions
• Tool: Immune Subtype Prediction — Use an ensemble model trained on all TCGA data to classify gene expression profiles from your own data into the six immune subtypes identified in Thorsson et al.

v1.0.1

Patch release with some minor fixes to CSS and README, along with updated utility function to fix selectInput bug (see issue #94) with optgroup labels.

v1.0.0

Signifies the initial public release of the Shiny-based iAtlas Portal, hosted at https://isb-cgc.shinyapps.io/shiny-iatlas/.