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NeighborhoodCoordination
Code accompanying our manuscript "Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front"spade
SPADE: Spanning Tree Progression of Density Normalized EventsCODEX
Image processing software for CODEX: driftcompensation, deconvolution, uploading and segmentationvortex
VorteX Clustering Environment - Java graphical tool for single-cell analysis, clustering and visualization. Latest release:citrus
Citrus Development CodecytofCore
R package for working with CyToF datascaffold
scaffoldREDSEA
bead-normalization
bead-based normalization of mass cytometry dataSpatialScore
R script for calculating the SpatialScore as described in our manuscript: "Immune cell topography predicts response to PD-1 blockade in cutaneous T cell lymphoma".RAPID
RAPID: a Real-time, GPU-Accelerated Parallelized Image processing software for large-scale multiplexed fluorescence microscopy Datacytospade
Cytoscape plugin for SPADETissueSchematics
Code accompanying the manuscript "Tissue Schematics map the specialization of immune tissue motifs and their appropriation by tumors"single-cell-debarcoder
deconvolution of barcoded CyTOF dataMatlabCytofUtilities
various scripts and functions that can be useful when working with mass (or flow) cytometry data in MatlabPLAYRDesign
A tool to design probes for the PLAYR technologyBioTekLiquidHandler
VWorks plugin for controlling BioTek liquid handlerscytof-backer-upper
Script for backing up CyTOF data to Google cloud storageMouseImmuneReference
A reference map of the mouse Immune SystemCODEXViewer
An ImageJ plugin to view and analyze CODEX images from the CODEXToolkit.CodexNapariViewer
A simple viewer for CODEX datasets developed using a python image analysis framework called napari.VWorks-Bioshake
VWorks plugin for Q.Instruments Bioshakediseffusion
Comprehensive comparison of dimensionality reduction data for single-cell dataLove Open Source and this site? Check out how you can help us