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

• UpdatedOct 5, 2024
• HTML

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

• UpdatedFeb 15, 2017
• R

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

• UpdatedSep 6, 2022
• R

A data-centric flow/mass cytometry automated analysis framework

• UpdatedJan 22, 2025
• Python

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

• UpdatedJul 11, 2023
• Julia

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

• UpdatedFeb 21, 2022
• R

R package for analysis of single-cell data using graphs

• UpdatedJun 8, 2023
• R

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

• UpdatedAug 10, 2021
• R

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

• UpdatedAug 5, 2022
• Jupyter Notebook

Official implementation of GateNet

• UpdatedJul 29, 2024
• Jupyter Notebook

An archived version of the cydar repository, seehttps://github.com/MarioniLab/cydar for the active version.

• UpdatedMay 25, 2017
• R

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

• UpdatedFeb 26, 2025
• Jupyter Notebook

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

• UpdatedDec 3, 2024
• Jupyter Notebook

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

• UpdatedDec 9, 2023
• Python

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.

• UpdatedFeb 25, 2021
• R

Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation

• UpdatedJan 23, 2024
• R

Fast auto-cleanup of CyTOF data

• UpdatedAug 12, 2021
• R

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

• UpdatedMar 3, 2020
• R

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

• UpdatedMay 23, 2017
• TeX

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

• UpdatedFeb 15, 2017
• R