nolanlab Goto Github PK

bead-normalization

bead-based normalization of mass cytometry data

biotekliquidhandler

VWorks plugin for controlling BioTek liquid handlers

cellvisionsegmenter

citrus

Citrus Development Code

codex

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

codexmsicreator

A visual studio project to create MSI for CODEX uploader and segmentation JAR

codexnapariviewer

A simple viewer for CODEX datasets developed using a python image analysis framework called napari.

codexserver

Run CODEX apps on the web: driftcompensation, deconvolution, segmentation, clustering and viewing

codexserversparkbuild

Project to deploy the CODEX server on the left and right computers in the nolan lab.

codexstacktrimmer

Trims the codex stacks leaving a specified number of slices around the given plane

codexupgrader

This tool is to help Codex users upgrade their processed Codex data from Nolan lab tiff or old format to the new image sequence format that is compatible to be used with MAV for analysis.

codexviewer

An ImageJ plugin to view and analyze CODEX images from the CODEXToolkit.

cytof-backer-upper

Script for backing up CyTOF data to Google cloud storage

cytofcore

R package for working with CyToF data

cytospade

Cytoscape plugin for SPADE

diseffusion

Comprehensive comparison of dimensionality reduction data for single-cell data

matlabcytofutilities

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

mouseimmunereference

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"

playrdesign

A tool to design probes for the PLAYR technology

rapid

RAPID: a Real-time, GPU-Accelerated Parallelized Image processing software for large-scale multiplexed fluorescence microscopy Data

rclusterpp

Memory efficient clustering in R for large datasets

redsea

sandbox

Accessory algorithms and data structures for multivariate single-cell analysis. VorteX and CODEX projects use this library

scaffold

scaffold

scaleinvdbv

Scale-invariant debarcoding algorithm for CyTOF data

scone

The SCONE algorithm

single-cell-debarcoder

deconvolution of barcoded CyTOF data

snail

SNAIL paper data

spade

SPADE: Spanning Tree Progression of Density Normalized Events