Repositories list

• 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

  •8•75•36•3•Updated Aug 14, 2025Aug 14, 2025

• FastReseg

  Public
  FastReseg for detection and correction of cell segmentation error based on spatial profile of transcripts.

  HTML

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  Other

  •2•10•10•1•Updated Aug 9, 2025Aug 9, 2025

• 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

  •18•44•35•4•Updated Aug 6, 2025Aug 6, 2025

• 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

  •6•22•18•1•Updated Jul 22, 2025Jul 22, 2025

• GeoMxWorkflows

  Public
  Workflows for analyzing data with the GeomxTools package and subsequent GeoMx related packages

  MIT License

  •9•5•7•2•Updated Jul 11, 2025Jul 11, 2025

• 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•10•9•0•Updated Jul 7, 2025Jul 7, 2025

• CellProfileLibrary

  Public
  Other

  •14•31•8•1•Updated May 19, 2025May 19, 2025

• DSPPlugins

  Public
  Repository for DSP Plugins

  HTML

  •3•10•9•0•Updated May 19, 2025May 19, 2025

• 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 May 19, 2025May 19, 2025

• 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

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  MIT License

  •9•40•23•0•Updated May 19, 2025May 19, 2025

• CelestaSignatureLibrary

  Public
  Other

  •0•3•0•0•Updated May 19, 2025May 19, 2025

• CosMxDACustomModules

  Public
  Repository for custom module scripts for SMIDA

  HTML

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  Other

  •1•13•3•0•Updated May 19, 2025May 19, 2025

• InSituCor

  Public
  InSituCor An R package for discovering modules of spatially correlated genes in spatial transcriptomics data.

  HTML

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  MIT License

  •0•8•10•0•Updated May 19, 2025May 19, 2025

• InSituType

  Public
  An R package for performing cell typing in SMI and other single cell data

  HTML

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  Other

  •15•39•24•0•Updated May 19, 2025May 19, 2025

• BrowserVegaLite

  Public
  JavaScript

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  MIT License

  •0•1•0•0•Updated Apr 22, 2025Apr 22, 2025

• sopa

  Public
  Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / etc)

  Python

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  BSD 3-Clause "New" or "Revised" License

  •36•0•0•0•Updated Apr 22, 2025Apr 22, 2025

• InSituCor-manuscript-analyses

  Public
  Reproducible analyses for the InSituCor manuscript

  R

  •0•1•0•0•Updated Jan 30, 2025Jan 30, 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

  •2•24•1•0•Updated Jan 24, 2025Jan 24, 2025

• 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•2•0•1•Updated Dec 5, 2024Dec 5, 2024

• tiledbsc

  Public
  Single-cell data structures in TileDB

  R

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  Other

  •3•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

• 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

  •15•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