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@Nanostring-Biostats

NanoString Technologies, Inc.

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  1. CosMx-Analysis-Scratch-Space 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 top…

    HTML 48 4

  2. GeomxTools GeomxTools Public

    Tools for NanoString GeoMx Digital Spatial Profiler data for reading DCC and PKC files to NanoStringGeomxSet class, Normalization and QC.

    R 37 16

  3. InSituType InSituType Public

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

    HTML 33 11

  4. SpatialOmicsOverlay SpatialOmicsOverlay Public

    Tools for analyzing data on the image from NanoString GeoMx Digital Spatial Profiler (DSP).

    R 18 4

  5. InSituCor InSituCor Public

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

    HTML 2

  6. FastReseg FastReseg Public

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

    HTML 7 1

Repositories

Showing 10 of 40 repositories
  • CosMx-Cell-Profiles Public

    CosMx Spatial Molecular Imager-derived cell profiles to aid in cell typing of SMI data.

    Nanostring-Biostats/CosMx-Cell-Profiles’s past year of commit activity
    R 7 1 1 1 Updated Jan 13, 2025
  • 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.

    Nanostring-Biostats/CosMx-Analysis-Scratch-Space’s past year of commit activity
    HTML 48 4 28 3 Updated Jan 10, 2025
  • CosMxDACustomModules Public

    Repository for custom module scripts for SMIDA

    Nanostring-Biostats/CosMxDACustomModules’s past year of commit activity
    HTML 12 0 2 0 Updated Dec 16, 2024
  • FastReseg Public

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

    Nanostring-Biostats/FastReseg’s past year of commit activity
    HTML 7 1 7 1 Updated Dec 16, 2024
  • InSituCor Public

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

    Nanostring-Biostats/InSituCor’s past year of commit activity
    HTML 2 0 10 1 Updated Dec 16, 2024
  • CelestaSignatureLibrary Public
    Nanostring-Biostats/CelestaSignatureLibrary’s past year of commit activity
    2 0 0 0 Updated Dec 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.)

    Nanostring-Biostats/SpatialDecon’s past year of commit activity
    R 34 MIT 9 23 0 Updated Dec 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.

    Nanostring-Biostats/GeoDiff’s past year of commit activity
    R 8 MIT 6 5 3 Updated Dec 16, 2024
  • CellProfileLibrary Public
    Nanostring-Biostats/CellProfileLibrary’s past year of commit activity
    30 14 8 1 Updated Dec 16, 2024
  • GeoMxWorkflows Public

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

    Nanostring-Biostats/GeoMxWorkflows’s past year of commit activity
    5 MIT 9 7 2 Updated Dec 16, 2024
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