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@CRI-iAtlas CRI iAtlas

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    28 repositories

    • iatlasManifests

      Public
      R
      •0•0•1•0•Updated Dec 6, 2024Dec 6, 2024

    • 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•12•27•0•Updated Dec 2, 2024Dec 2, 2024

    • ImmuneSubtypeClassifier

      Public
      An R package for classification of immune subtypes, in cancer, using gene expression data.
      R
      •
      Other
      •23•43•10•0•Updated Nov 7, 2024Nov 7, 2024

    • iAtlasSchema

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

    • iatlas.modules2

      Public
      R
      •
      Other
      •1•0•0•0•Updated Sep 25, 2024Sep 25, 2024

    • iatlas-notebooks

      Public
      Collection of R notebooks to enable local iAtlas plotting and functionality.
      Jupyter Notebook
      •0•2•1•0•Updated Sep 24, 2024Sep 24, 2024

    • iatlasGraphQLClient

      Public
      R
      •
      Other
      •1•0•3•0•Updated Aug 9, 2024Aug 9, 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 imaging data. No training dataset with cell type labels is required.
      R
      •
      Apache License 2.0
      •11•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-biologyimmunology
      R
      •
      Apache License 2.0
      •12•48•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
      •28•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