A Python toolkit for flow cytometry analysis supporting GatingML and FlowJo workspaces

Easily install and load packages from the tidyomics ecosystem

A Python library for reading and writing Flow Cytometry Standard (FCS) files

Biology-driven deep generative model for cell-type annotation in cytometry. Scyan is an interpretable model that also corrects batch-effect and can be used for debarcoding or population discovery.

A data-centric flow/mass cytometry automated analysis framework

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

Image Mass Cytometry analysis pipeline

Fast embedding ot multidimensional datasets, great for cytometry data

FlowUtils is a Python package containing various utility functions related to flow cytometry analysis, primarily focused on compensation and transformation tasks commonly used within the flow community.

An R package for analyzing high-dimensional cytometry data using the tidyverse.

an interactive explorer for flow cytometry data

A clustering algorithm that will perform clustering on each of a time-series of discrete datasets, and explicitly track the evolution of clusters over time.

SuperCell for Cytometry data

Single-cell dimensionality reduction toolkit

Import script needed to build FluPRINT database from source :computer:

Code and results from TotalSeqC antibody titration and pipeline benchmarking for CITE-seq experiments

Official implementation of GateNet

Single-cell dimensionality reduction evaluation and benchmarking toolkit

Integration of multi-batch cytometry datasets

Temporal clustering and tracking algorithm which fuses on FlowSOM and ChronoClust, specifically designed for analysing temporal cytometry data

Histology Topography Cytometry Analysis Toolbox (histoCAT) for Web.

Pipeline for flow cytometry anlaysis

Algorithms for the selection of fluorescent reporters.

Pipeline for analysing and visualising CyTOF datasets, with a focus on PTM signalling networks.

Tools for Imaging Flow Cytometry

An R Interactive Shiny Application for the Analysis of Imaging and Conventional Flow Cytometry

Shape-Out has been superseded by Shape-Out 2.

An R package for visualization and relational analysis of cell states, based on the Mapper algorithm from topological data analysis.

An R package to apply Batch Normalization to cytometry

Flow Cytometry analysis in R | Proteomics