A computational toolkit in R for the integration, exploration, and analysis of high-dimensional single-cell cytometry and imaging data.

R package for pre-processing of mass and flow cytometry data

R scripts to reproduce analyses in our paper comparing clustering methods for high-dimensional cytometry data

A data-centric flow/mass cytometry automated analysis framework

Huge-scale, high-performance flow cytometry clustering in Julia

R package for interactive visualization and analysis of single-cell data

R package for analysis of single-cell data using graphs

This repository extends scanpy to handle flow and mass cytometry data.

Official implementation of GateNet

R package to cluster single-cell data and generate features that can be used for model building

Rapid and efficient image preprocessing pipeline for multiplexed spatial proteomics. Code to compare several techniques to denoise Imaging Mass cytometry

An archived version of the cydar repository, see https://github.com/MarioniLab/cydar for the active version.

Single Cell Outlier Selector - quickly find outliers in your single-cell data

Fast auto-cleanup of CyTOF data

Novel ultrafast suite for high-throughput & high-content multiparameter screening as in drug discovery. It has unique modules for QC, bias correction, similarity measurement, clustering and visualization. It can process hundreds of samples with many markers in a few hours not days & circumvents bath effect. It couples with any plate reader.

Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation

Rapid and efficient image preprocessing pipeline for multiplexed spatial proteomics. Code to compare several techniques to denoise Imaging Mass cytometry

The multi-sample Gaussian mixture model (MSGMM) is a clustering model adapted to fitting multiple samples simultaneously using the EM algorithm.

Code and manuscript files for Aaron and Arianne's differential abundance methodology manuscript.

Plots log histograms of FCS files like CyTOF's PlotViewer program

R script for summarising paramater / channel intensity from flow or mass cytometry data

Automated detection of technical anomalies in cytometry data

Code for analysis of single cell signaling network kinetics from flow cytometry (CyTOF) datasets

R Script for reading CyTOF or flow cytometry data (FCS) and generating plots like Cytobank

Batch effect correction and automated gating of CyTOF data

Very fast method to read number of events from some / all FCS files in a directory

Plots the NRS (non-redundancy score) of selected markers from one or more FCS files

Opens two or more FCS files and creates new files that contain only the Channels common to all.

A handy spreadsheet for looking up elemental isotopes by symbol or mass.

Plots the MDS (Multi-dimensional scaling) of 3 or more FCS files.