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

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

R package for pre-processing of mass and flow 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.

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

An archived version of the cydar repository, see https://github.com/MarioniLab/cydar for the active version.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

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

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

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

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

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

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