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
Official implementation of GateNet
R package for analysis of single-cell data using graphs
R package for interactive visualization and analysis of single-cell data
R package to cluster single-cell data and generate features that can be used for model building
This repository extends scanpy to handle flow and mass cytometry data.
Rapid and efficient image preprocessing pipeline for multiplexed spatial proteomics. Code to compare several techniques to denoise Imaging Mass cytometry
Plain-text, git-tracked lab notebook for reproducible bioinformatics — keeps figures in your Markdown notes in sync with the R & Python code that made them, and re-renders them headlessly from the notebook itself. Built for single-cell / CyTOF / flow cytometry; works with Obsidian, Quarto & Jupyter.
An archived version of the cydar repository, see https://github.com/MarioniLab/cydar for the active version.
Interactive flow and mass cytometry gating in R for SingleCellExperiment and GatingSet objects. Browser version: https://gate-lab.github.io/
Automated detection of technical anomalies in cytometry data
Rapid and efficient image preprocessing pipeline for multiplexed spatial proteomics. Code to compare several techniques to denoise Imaging Mass cytometry
Single Cell Outlier Selector - quickly find outliers in your single-cell data
Rapid and efficient image preprocessing pipeline for multiplexed spatial proteomics. Code to compare several techniques to denoise Imaging Mass cytometry
Browser-based software for manual gating of flow and mass cytometry data, with FlowJo workspace and Gating-ML exchange, compensation, statistics and figure export.
Fast auto-cleanup of CyTOF data
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