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@CRI-iAtlas CRI iAtlas

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    Repositories list

    28 repositories

    • iatlas-app

      Public
      R Shiny app for CRI iAtlas, an interactive web portal for exploring immuno-oncology data. (iAtlas portal 2022 and beyond)
      R
      •
      Other
      •3•15•22•0•Updated May 15, 2026May 15, 2026

    • iatlas-notebooks

      Public
      Collection of R notebooks to enable local iAtlas plotting and functionality.
      Jupyter Notebook
      •2•2•2•0•Updated Mar 17, 2026Mar 17, 2026

    • ImmuneSubtypeClassifier

      Public
      An R package for classification of immune subtypes, in cancer, using gene expression data.
      R
      •
      Other
      •21•48•11•0•Updated Mar 6, 2026Mar 6, 2026

    • iatlasManifests

      Public
      R
      •0•0•2•0•Updated Dec 15, 2025Dec 15, 2025

    • iatlas.modules2

      Public
      R
      •
      Other
      •1•0•0•0•Updated Oct 15, 2025Oct 15, 2025

    • iatlasGraphQLClient

      Public
      R
      •
      Other
      •1•0•4•0•Updated Jan 22, 2025Jan 22, 2025

    • iAtlasSchema

      Public
      The data model schema for the iAtlas database
      0•0•1•0•Updated Oct 8, 2024Oct 8, 2024

    • iatlas.modules

      Public
      R
      •
      Other
      •1•0•0•0•Updated Aug 5, 2024Aug 5, 2024

    • scRNAseq-dev

      Public
      Code to prepare single-cell RNA-seq datasets for ingress in iAtlas
      Jupyter Notebook
      •0•0•0•0•Updated Jun 28, 2024Jun 28, 2024

    • nf-pseudobulk

      Public
      Nextflow pipeline to compute GSEA for pseudobulk scRNAseq
      Nextflow
      •0•0•0•0•Updated Apr 17, 2024Apr 17, 2024

    • iatlas-workflows

      Public
      cwl workflows for public tools
      Common Workflow Language
      •4•2•0•0•Updated May 23, 2023May 23, 2023

    • pret

      Public
      Clojure
      •
      Apache License 2.0
      •3•0•0•0•Updated Mar 28, 2023Mar 28, 2023

    • CELESTA

      Public
      Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information for multiplexed in situ…
      R
      •
      Apache License 2.0
      •13•0•0•0•Updated Jan 21, 2023Jan 21, 2023

    • iatlas.api.client

      Public
      R
      •
      Other
      •2•0•0•0•Updated Apr 13, 2022Apr 13, 2022

    • iatlas-feather-files

      Public
      R
      •0•0•0•0•Updated Aug 23, 2021Aug 23, 2021

    • test-notebooks

      Public
      open tests
      Jupyter Notebook
      •0•0•0•0•Updated Aug 10, 2021Aug 10, 2021

    • TCGA

      Public
      Code for TCGA spefic analyses
      R
      •0•0•0•0•Updated Jun 9, 2021Jun 9, 2021

    • shiny-iatlas

      Public
      An interactive web portal for exploring immuno-oncology data. This repo now superseded by iatlas-app
      genomicscancersystems-biology
      genomicscancersystems-biologyimmunology
      R
      •
      Apache License 2.0
      •12•51•0•0•Updated Feb 26, 2021Feb 26, 2021

    • ICGC

      Public
      Repo for ICGC specific code
      R
      •0•0•0•0•Updated Feb 15, 2021Feb 15, 2021

    • cyjShiny

      Public
      An R/shiny widget for cytoscape.js
      JavaScript
      •
      MIT License
      •29•0•0•0•Updated Nov 11, 2020Nov 11, 2020

    • iatlas-data

      Public archive
      MOVED TO GITLAB -> https://gitlab.com/cri-iatlas/iatlas-data.git
      R
      •0•1•8•0•Updated Jun 25, 2020Jun 25, 2020

    • rmarkdown-server

      Public
      prototype HTTP server to dynamically render parameterized Rmarkdown files
      R
      •0•0•0•0•Updated Feb 24, 2020Feb 24, 2020

    • rmarkdown-server-client

      Public
      React-based client for presenting a friendly UI for the rmarkdown-server
      JavaScript
      •0•0•0•0•Updated Feb 24, 2020Feb 24, 2020

    • discourse-docker-image

      Public
      0•0•0•0•Updated May 23, 2018May 23, 2018

    • shiny-heatmap-viewer

      Public
      R
      •0•1•0•0•Updated Jan 18, 2018Jan 18, 2018

    • shiny-dockstore-browser

      Public
      shiny tool for browsing dockstore entries
      R
      •1•0•0•0•Updated Jan 11, 2018Jan 11, 2018

    • irwg-tool-mitcr

      Public
      Dockerized MiTCR tool for Dockstore
      0•0•0•0•Updated Dec 5, 2017Dec 5, 2017

    • synapse-utils

      Public
      Scripts for surveying, summarizing, and organizing PanImmune data in Synapse
      HTML
      •0•0•0•0•Updated Oct 14, 2017Oct 14, 2017
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