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bioconductor2021

browservegalite

celestasignaturelibrary

cellprofilelibrary

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.

cosmx-cell-profiles

cosmx-minervastory-01

This repo is for visualizing an in-progress Minerva Story for CosMx.

cosmxdacustommodules

Repository for custom module scripts for SMIDA

covid-convalescent-ncounter-analysis

Analyses for Gedda & Danaher et al., "Longitudinal Transcriptional Analysis of Peripheral Blood Leukocytes in COVID Convalescent Donors"

dspplugins

Repository for DSP Plugins

fastreseg

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

finalcolonstory

finallymphnodestory

finalpancreasstory

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.

geomx-imagej-macros

geomxtools

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

geomxworkflows

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

humanbrain

humanliverstory

immunedeconbenchmark

insitucor

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

insitucor-manuscript-analyses

Reproducible analyses for the InSituCor manuscript

insitutype

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

insitutype-manuscript-analyses

Analyses for the manuscript, "Insitutype: likelihood-based cell typing for single cell spatial transcriptomics"

kidneystory

Minerva Kidney Story

minerva-author

Tool to create images and configuration files for Minerva-Story

minerva-author-ui

Minerva Author is an authoring tool used to create Minerva narrated stories via selection of specific channel groupings and image views.

mousebrain

mousedevtest