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    40 repositories

    • CosMx-Analysis-Scratch-Space

      Public
      This repository is an exploratory resource to accelerate opensource analysis of CosMx® Spatial Molecular Imager (SMI) data. Contained here are and writeups and vignettes addressing a variety of topics discussed when analyzing single-cell spatial data.
      HTML
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      Other
      •4•48•28•3•Updated Jan 16, 2025Jan 16, 2025

    • CosMx-Cell-Profiles

      Public
      CosMx Spatial Molecular Imager-derived cell profiles to aid in cell typing of SMI data.
      R
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      Other
      •1•7•1•1•Updated Jan 13, 2025Jan 13, 2025

    • CosMxDACustomModules

      Public
      Repository for custom module scripts for SMIDA
      HTML
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      Other
      •0•12•2•0•Updated Dec 16, 2024Dec 16, 2024

    • FastReseg

      Public
      FastReseg for detection and correction of cell segmentation error based on spatial profile of transcripts.
      HTML
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      Other
      •1•7•7•1•Updated Dec 16, 2024Dec 16, 2024

    • InSituCor

      Public
      InSituCor An R package for discovering modules of spatially correlated genes in spatial transcriptomics data.
      HTML
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      Other
      •0•2•10•1•Updated Dec 16, 2024Dec 16, 2024

    • CelestaSignatureLibrary

      Public
      Other
      •0•2•0•0•Updated Dec 16, 2024Dec 16, 2024

    • SpatialDecon

      Public
      The SpatialDecon library implements the SpatialDecon algorithm for mixed cell deconvolution in spatial gene expression datasets. (This algorithm also works in bulk expression profiling data.)
      R
      •
      MIT License
      •9•35•23•0•Updated Dec 16, 2024Dec 16, 2024

    • GeoDiff

      Public
      GeoDiff, an R package for count generating models for analyzing Geomx RNA data. Note that this version of the package is still under development, undergoing submission process to Bioconductor 3.14 release and still needs to complete NanoString internal verification process.
      R
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      MIT License
      •6•8•5•3•Updated Dec 16, 2024Dec 16, 2024

    • CellProfileLibrary

      Public
      Other
      •14•30•8•1•Updated Dec 16, 2024Dec 16, 2024

    • GeoMxWorkflows

      Public
      Workflows for analyzing data with the GeomxTools package and subsequent GeoMx related packages
      MIT License
      •9•5•7•2•Updated Dec 16, 2024Dec 16, 2024

    • NanoStringNCTools

      Public
      Tools for NanoString Technologies nCounter Technology for reading RCC files into an ExpressionSet derived object, QC and normalization.
      R
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      MIT License
      •6•9•9•0•Updated Dec 16, 2024Dec 16, 2024

    • DSPPlugins

      Public
      Repository for DSP Plugins
      HTML
      •4•10•9•0•Updated Dec 16, 2024Dec 16, 2024

    • SpatialOmicsOverlay

      Public
      Tools for analyzing data on the image from NanoString GeoMx Digital Spatial Profiler (DSP).
      visualizationimage-processingr-package
      R
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      MIT License
      •4•18•18•0•Updated Dec 16, 2024Dec 16, 2024

    • InSituType

      Public
      An R package for performing cell typing in SMI and other single cell data
      HTML
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      Other
      •11•33•22•0•Updated Dec 16, 2024Dec 16, 2024

    • GeomxTools

      Public
      Tools for NanoString GeoMx Digital Spatial Profiler data for reading DCC and PKC files to NanoStringGeomxSet class, Normalization and QC.
      R
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      MIT License
      •16•37•34•1•Updated Dec 16, 2024Dec 16, 2024

    • childhood-onset-lupus-nephritis-analyses

      Public
      Analyses from the manuscript, "Single cell spatial transcriptomic profiling of childhood-onset lupus nephritis reveals complex interactions between kidney stroma and infiltrating immune cells"
      R
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      MIT License
      •0•1•0•1•Updated Dec 5, 2024Dec 5, 2024

    • InSituCor-manuscript-analyses

      Public
      Reproducible analyses for the InSituCor manuscript
      R
      •0•1•0•0•Updated Mar 29, 2024Mar 29, 2024

    • tiledbsc

      Public
      Single-cell data structures in TileDB
      R
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      Other
      •4•0•0•0•Updated Mar 12, 2024Mar 12, 2024

    • SOOBiocWorkshop

      Public
      Dockerfile
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      Other
      •2•1•0•0•Updated May 21, 2023May 21, 2023

    • BrowserVegaLite

      Public
      JavaScript
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      MIT License
      •0•1•0•0•Updated Mar 10, 2023Mar 10, 2023

    • HumanLiverStory

      Public
      HTML
      •0•2•0•0•Updated Feb 27, 2023Feb 27, 2023

    • cosmx-minervastory-01

      Public
      This repo is for visualizing an in-progress Minerva Story for CosMx.
      HTML
      •0•1•0•0•Updated Nov 8, 2022Nov 8, 2022

    • Insitutype-manuscript-analyses

      Public
      Analyses for the manuscript, "Insitutype: likelihood-based cell typing for single cell spatial transcriptomics"
      R
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      MIT License
      •4•0•0•0•Updated Oct 28, 2022Oct 28, 2022

    • SpatialResolution

      Public
      This repository contains code used for analyses and visualizations for the paper Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling published in Genome Research
      R
      •2•3•0•1•Updated Aug 22, 2022Aug 22, 2022

    • minerva-author

      Public
      Tool to create images and configuration files for Minerva-Story
      Python
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      MIT License
      •14•1•0•0•Updated Jun 6, 2022Jun 6, 2022

    • humanBrain

      Public
      HTML
      •0•1•0•0•Updated May 18, 2022May 18, 2022

    • MouseDevTest

      Public
      HTML
      •0•0•0•0•Updated Apr 27, 2022Apr 27, 2022

    • finalLymphNodeStory

      Public
      HTML
      •0•0•0•0•Updated Apr 22, 2022Apr 22, 2022

    • finalColonStory

      Public
      HTML
      •0•0•0•0•Updated Apr 22, 2022Apr 22, 2022

    • NanoStringExperiment

      Public
      R
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      MIT License
      •1•0•1•0•Updated Apr 20, 2022Apr 20, 2022