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Cell population identification software tools | Flow cytometry

In analyzing flow cytometry data, one fundamental question is how to divide the cells into distinct subsets with the phenotypes defined by the fluorescent intensity of the cell surface or intracellular markers. Source text: Ge and Sealfon, 2012.

FlowCAP
Desktop

FlowCAP Flow cytometry: Critical Assessment of Population identification methods

Advances the development of computational methods for the identification of…

Advances the development of computational methods for the identification of cell populations of interest in FCM data. FlowCAP provides the means to objectively test and compare different methods. The…

SPADEVizR
Desktop

SPADEVizR

Designed for the visualization, analysis and integration of cell clustering…

Designed for the visualization, analysis and integration of cell clustering results. Clusters having similar cell abundance profiles can be classified, using various methods such as k-means.…

flowCL
Desktop

flowCL

Performs semantic labelling of cell populations based on their surface markers…

Performs semantic labelling of cell populations based on their surface markers and applied it to labelling of the Federation of Clinical Immunology Societies Human Immunology Project Consortium…

VorteX
Desktop

VorteX

Facilitates the exploration of single-cell analysis of complex systems. VorteX…

Facilitates the exploration of single-cell analysis of complex systems. VorteX provides a rapid, reliable approach to manage cell subset analysis that maximizes automation. It can process large…

CellSort
Desktop

CellSort

Identifies optimal sorting gates based on machine learning using positive and…

Identifies optimal sorting gates based on machine learning using positive and negative control populations. CellSort can take advantage of more than two dimensions to enhance the ability to…

seaflow_cluster
Desktop

seaflow_cluster

A Gaussian mixture model with partitioning approach for classification of…

A Gaussian mixture model with partitioning approach for classification of large-scale, high-frequency flow cytometry data. This approach outperforms current state-of-the-art cytometry classification…

SigClust
Desktop

SigClust Single-Cell Clustering

Allows users to identify homogeneous cellular populations from flow cytometry…

Allows users to identify homogeneous cellular populations from flow cytometry datasets. SigClust uses a combination of t-distributed Stochastic Neighbor Embedding (t-SNE). It is able to identify…

flowDensity
Desktop

flowDensity

Facilitates reproducible, high-throughput analysis of flow cytometry data by…

Facilitates reproducible, high-throughput analysis of flow cytometry data by automating a predefined manual gating approach. The algorithm is based on a sequential bivariate gating approach that…

BayesFlow
Desktop

BayesFlow

A pipeline for latent modeling of flow cytometry cell populations built upon a…

A pipeline for latent modeling of flow cytometry cell populations built upon a Bayesian hierarchical model. The model systematizes variation in location as well as shape. Expert knowledge can be…

Cell…
Desktop
SamSPECTRAL
Desktop

SamSPECTRAL

Identifies overlapping populations that are generally hard to identify by…

Identifies overlapping populations that are generally hard to identify by manual gating that uses sequential two dimensional visualizations of the data, based on a multidimensional clustering…

flowMatch
Desktop

flowMatch

A package based on a hierarchical algorithm to first match the corresponding…

A package based on a hierarchical algorithm to first match the corresponding clusters across samples for producing robust meta-clusters, and to then construct a high-dimensional template as a…

flowClust
Desktop

flowClust

A package dedicated to FCM gating analysis, addressing the increasing demand…

A package dedicated to FCM gating analysis, addressing the increasing demand for software capable of processing and analyzing the voluminous amount of FCM data efficiently via an objective,…

EMMIX-JCM
Desktop

EMMIX-JCM

Joint clustering and matching (JCM) is a multi-level framework for simultaneous…

Joint clustering and matching (JCM) is a multi-level framework for simultaneous modeling and registration of populations across a cohort. JCM models every population with a robust multivariate…

flowCHIC
Desktop

flowCHIC

Allows users to detect flow cytometric data that use histogram information.…

Allows users to detect flow cytometric data that use histogram information. flowCHIC works about information coming from complex microbial communities.

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.…

SWIFT
Desktop

SWIFT Scalable Weighted Iterative Flow-clustering Technique

Provide tools for automating analysis for massive high-dimensional datasets.…

Provide tools for automating analysis for massive high-dimensional datasets. SWIFT is based on a multi-stage framework for clustering with features that are motivated in particular by the…

CDP
Desktop

CDP

An integration of Bayesian non-parametric mixture models, massively parallel…

An integration of Bayesian non-parametric mixture models, massively parallel computing on GPUs and software development in Python to provide an extensible toolkit for automated statistical analysis…

FlowVB
Desktop

FlowVB

Mixture models are popular as an automated means of gating flow cytometry data,…

Mixture models are popular as an automated means of gating flow cytometry data, as mixtures of Gaussian densities, or more robust Student-t densities, can cluster flow data in a statistically…

flowMeans
Desktop

flowMeans

A package based on a time-efficient and accurate method for automated…

A package based on a time-efficient and accurate method for automated identification of cell populations in flow cytometry (FCM) data based on K-means clustering. Unlike traditional K-means,…

flowMerge
Desktop

flowMerge

A framework for the identification of cell subpopulations in flow cytometry…

A framework for the identification of cell subpopulations in flow cytometry data based on merging mixture components using the flowClust methodology. flowMerge is based on a cluster merging algorithm…

flowCyBar
Desktop

flowCyBar

A package to analyze flow cytometric data using gate information to follow…

A package to analyze flow cytometric data using gate information to follow population/community dynamics.

flowFP
Desktop

flowFP

A package for the analysis of flow cytometry data. flowFP provides tools to…

A package for the analysis of flow cytometry data. flowFP provides tools to transform raw flow cytometry data into a form suitable for direct input into conventional statistical analysis and…

flowPeaks
Desktop

flowPeaks

A fast and automatic clustering to classify the cells into subpopulations based…

A fast and automatic clustering to classify the cells into subpopulations based on finding the peaks from the overall density function generated by K-means.

ADICyt
Desktop
Web

ADICyt

A desktop software application for effective analysis of flow cytometry data.…

A desktop software application for effective analysis of flow cytometry data. Great emphasis is placed on leveraging machine learning methods for automated data analysis and population discovery…

FLOCK
Desktop

FLOCK FLOw Clustering without K

Uses a density-based clustering approach to algorithmically identify…

Uses a density-based clustering approach to algorithmically identify biologically relevant cell populations from multiple samples in an unbiased fashion, thereby eliminating operator-dependent…

flowKoh
Desktop

flowKoh

It is specifically designed and developed for cell population identification in…

It is specifically designed and developed for cell population identification in flow cytometry data. It includes the R package kohonen which was applied to cluster three FlowCAP datasets in…

X-Cyt
Desktop

X-Cyt

Follows a user-designed scheme and template to partition cytometric data in two…

Follows a user-designed scheme and template to partition cytometric data in two or more dimensions for identifying cell populations of interest.

FLAME
Desktop

FLAME FLow analysis with Automated Multivariate Estimation

Uses finite mixture model clustering techniques with novel algorithms and…

Uses finite mixture model clustering techniques with novel algorithms and models to define and characterize discrete populations in flow cytometric data. A distinguishing feature of FLAME is its use…

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