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GeomxTools
Tools for NanoString GeoMx Digital Spatial Profiler data for reading DCC and PKC files to NanoStringGeomxSet class, Normalization and QC.SpatialDecon
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.)InSituType
An R package for performing cell typing in SMI and other single cell dataCosMx-Analysis-Scratch-Space
This repository is an exploratory resource to accelerate opensource analysis of CosMxâ„¢ Spatial Molecular Imager (SMI) data. Contained here are and writeups and vignettes addressing a variety of topics discussed when analyzing single-cell spatial data.CellProfileLibrary
SpatialOmicsOverlay
Tools for analyzing data on the image from NanoString GeoMx Digital Spatial Profiler (DSP).SpatialDecon-manuscript-analyses
Holds the code and data to reproduce the analyses of Danaher & Kim et a;, "Advances in mixed cell deconvolution enable quantification of cell types in spatially-resolved gene expression data"CosMxDACustomModules
Repository for custom module scripts for SMIDADSPPlugins
Repository for DSP PluginsNanoStringNCTools
Tools for NanoString Technologies nCounter Technology for reading RCC files into an ExpressionSet derived object, QC and normalization.GeoDiff
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.CosMx-Cell-Profiles
GeoMxWorkflows
Workflows for analyzing data with the GeomxTools package and subsequent GeoMx related packagesSpatialResolution
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 ResearchFastReseg
FastReseg for detection and correction of cell segmentation error based on spatial profile of transcripts.HumanLiverStory
InSituCor
InSituCor An R package for discovering modules of spatially correlated genes in spatial transcriptomics data.BrowserVegaLite
humanBrain
cosmx-minervastory-01
This repo is for visualizing an in-progress Minerva Story for CosMx.SOOBiocWorkshop
ImmuneDeconBenchmark
InSituCor-manuscript-analyses
Reproducible analyses for the InSituCor manuscriptBioconductor2021
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