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Mass cytometry tools

Mass cytometry addresses the analytical challenges of polychromatic flow cytometry by using metal atoms as tags rather than fluorophores and atomic mass spectrometry as the detector rather than photon optics.

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Wishbone
Desktop

Wishbone

Aligns single cells from differentiation systems with bifurcating branches.…

Aligns single cells from differentiation systems with bifurcating branches. Wishbone pinpoints bifurcation points and labels each cell as pre-bifurcation or as one of two post-bifurcation cell fates…

viSNE
Desktop

viSNE

A tool that allows one to map high-dimensional cytometry data onto two…

A tool that allows one to map high-dimensional cytometry data onto two dimensions, yet conserve the high-dimensional structure of the data.

Wanderlust
Desktop

Wanderlust

A graph-based trajectory detection algorithm that receives multiparameter…

A graph-based trajectory detection algorithm that receives multiparameter single-cell events as input and maps them onto a one-dimensional developmental trajectory. Cells are ordered along a…

Cytofkit
Web
Desktop

Cytofkit

Enables simultaneous illustration of cellular diversity and progression.…

Enables simultaneous illustration of cellular diversity and progression. Cytofkit firstly performs data pre-processing, and enables combined analysis of multiple Flow Cytometry Standard (FCS) files.…

cydar
Desktop

cydar

Detects ‘differentially abundant’ populations between samples and groups in…

Detects ‘differentially abundant’ populations between samples and groups in mass cytometry data. Cydar is a computational strategy to perform differentially abundant (DA) analyses of mass…

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densityCut
Desktop

densityCut

A density-based clustering algorithm, which is both time- and space-efficient…

A density-based clustering algorithm, which is both time- and space-efficient and proceeds as follows: densityCut first roughly estimates the densities of data points from a K-nearest neighbour graph…

MetaCyto
Desktop

MetaCyto

Enables automated meta-analysis of cytometry datasets, including both…

Enables automated meta-analysis of cytometry datasets, including both conventional flow and mass cytometry (CyTOF) data. MetaCyto combines clustering methods and a silhouette scanning method. The…

ACDC
Desktop

ACDC Automated Cell-type Discovery and Classification

Automates the classification of canonical cell populations and highlights novel…

Automates the classification of canonical cell populations and highlights novel cell types in mass cytometry data. ACDC provides accurate and reliable estimations compared to manual gating results.…

FlowSOM
Desktop

FlowSOM

Analyzes flow or mass cytometry data using a self-organizing map. Using a…

Analyzes flow or mass cytometry data using a self-organizing map. Using a two-level clustering and star charts, FlowSOM helps to obtain a clear overview of how all markers are behaving on all cells,…

DeepCyTOF
Algorithm

DeepCyTOF

A standardization approach for gating based on a multi-autoencoder neural…

A standardization approach for gating based on a multi-autoencoder neural network. DeepCyTOF requires labeled cells from only a single sample. It is based on domain adaptation principles and is a…

ACCENSE
Desktop
Citrus
Desktop

Citrus

A package for identifying clusters of cells in multidimensional flow cytometry…

A package for identifying clusters of cells in multidimensional flow cytometry data associated with an experimental or clinical endpoint of interest. A Citrus analysis generally involves four steps:…

one-dimensional…
Desktop

one-dimensional Soli-Expression by Nonlinear Stochastic Embedding

Facilitates the dimensional reduction method based on the t-distributed…

Facilitates the dimensional reduction method based on the t-distributed stochastic neighbor embedding (t-SNE) algorithm. oneSENSE is a graphical user interface (GUI) for categorical analysis of mass…

CATALYST
Desktop

CATALYST Cytometry dATa anALYSis Tools

Provides tools for pre-processing and analysis of cytometry data, including…

Provides tools for pre-processing and analysis of cytometry data, including compensation and in particular, an improved implementation of the single-cell deconvolution algorithm. CATALYST is a…

immunoClust
Desktop

immunoClust

An automated analysis pipeline for uncompensated fluorescence and mass…

An automated analysis pipeline for uncompensated fluorescence and mass cytometry data, which consists of two parts. First, cell events of each sample are grouped into individual clusters.…

CYT
Desktop

CYT

An interactive visualization tool designed for the analysis of viSNE maps and…

An interactive visualization tool designed for the analysis of viSNE maps and the high-dimensional mass or flow cytometry data from which these maps were projected.

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