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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 data

CosMx-Analysis-Scratch-Space

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.

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 SMIDA

DSPPlugins

Repository for DSP Plugins

NanoStringNCTools

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 packages

SpatialResolution

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

FastReseg

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.

CelestaSignatureLibrary

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 manuscript

Bioconductor2021