nolanlab/MouseImmuneReference

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Created over 9 years ago
Updated over 9 years ago

nolanlab/MouseImmuneReference

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A reference map of the mouse Immune System

NeighborhoodCoordination

Code accompanying our manuscript "Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front"

Jupyter Notebook

spade

SPADE: Spanning Tree Progression of Density Normalized Events

CODEX

Image processing software for CODEX: driftcompensation, deconvolution, uploading and segmentation

vortex

VorteX Clustering Environment - Java graphical tool for single-cell analysis, clustering and visualization. Latest release:

citrus

Citrus Development Code

cytofCore

R package for working with CyToF data

Rclusterpp

Memory efficient clustering in R for large datasets

scaffold

REDSEA

Jupyter Notebook

bead-normalization

bead-based normalization of mass cytometry data

SpatialScore

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 Data

cytospade

Cytoscape plugin for SPADE

TissueSchematics

Code accompanying the manuscript "Tissue Schematics map the specialization of immune tissue motifs and their appropriation by tumors"

Jupyter Notebook

single-cell-debarcoder

deconvolution of barcoded CyTOF data

MatlabCytofUtilities

various scripts and functions that can be useful when working with mass (or flow) cytometry data in Matlab

PLAYRDesign

A tool to design probes for the PLAYR technology

BioTekLiquidHandler

VWorks plugin for controlling BioTek liquid handlers

cytof-backer-upper

Script for backing up CyTOF data to Google cloud storage

CODEXViewer

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 Bioshake

diseffusion

Comprehensive comparison of dimensionality reduction data for single-cell data