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Other flow cytometry software tools and databases

RchyOptimyx
Desktop

RchyOptimyx cellular hieraRCHY OPTIMization

Constructs cellular hierarchies by combining automated gating with dynamic…

Constructs cellular hierarchies by combining automated gating with dynamic programming and graph theory to provide the best gating strategies to identify a target population to a desired level of…

ShAPE-DALSP
Desktop

ShAPE-DALSP

A model-based analysis method for carboxyfluorescein succinimidyl ester (CFSE)…

A model-based analysis method for carboxyfluorescein succinimidyl ester (CFSE) time-series data. ShAPE-DALSP uses a flexible description of proliferating cell populations, namely, a division-, age-…

FloReMi
Desktop

FloReMi

Criticizes the recent FlowCAP IV challenge. The FloReMi approach consists of…

Criticizes the recent FlowCAP IV challenge. The FloReMi approach consists of four steps: (1) the data is preprocessed, (2) many features are extracted (i.e., properties pertaining to certain cell…

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…

flowType
Desktop

flowType

A package based on a computational approach that automatically reveals all…

A package based on a computational approach that automatically reveals all possible cell subsets. By using flowType, from tens of thousands of subsets, those that correlate strongly with clinical…

flowViz
Desktop

flowViz

A package that provides graphical diagnostics and quality assessment…

A package that provides graphical diagnostics and quality assessment applications. flowViz adapts principles of Trellis graphics to FCM data. It provides useful visualizations that can aid automated…

MIMOSA
Desktop

MIMOSA

A Bayesian hierarchical framework based on a beta-binomial mixture model for…

A Bayesian hierarchical framework based on a beta-binomial mixture model for testing for differential biomarker expression using single-cell assays. MIMOSA allows the inference to be subject…

flowTime
Desktop

flowTime

Allows the analysis of dynamic and steady state experiments. flowTime…

Allows the analysis of dynamic and steady state experiments. flowTime simplifies the annotation of flow cytometry data with experimental metadata. It includes several functions for gate sets to…

COMPASS
Desktop

COMPASS

A statistical framework that enables unbiased analysis of antigen-specific…

A statistical framework that enables unbiased analysis of antigen-specific T-cell subsets. COMPASS uses a Bayesian hierarchical framework to model all observed cell-subsets and select the most likely…

plateCore
Desktop

plateCore

Creates methods and data structures for processing large, plate-based FCM data…

Creates methods and data structures for processing large, plate-based FCM data sets by taking advantage of the functionality in flowCore and flowViz. plateCore makes it easier to integrate textual…

flowMap
Desktop

flowMap

Quantifies the similarity of cell populations across multiple flow cytometry…

Quantifies the similarity of cell populations across multiple flow cytometry samples using a nonparametric multivariate statistical test. flowMap is able to map cell populations of different size,…

flowPlots
Desktop

flowPlots

A package which offers graphical displays with embedded statistical tests for…

A package which offers graphical displays with embedded statistical tests for gated ICS flow cytometry data, and a data class which stores "stacked" data and has methods for computing…

CytoSPADE
Desktop

CytoSPADE

A high-performance implementation of an interface for the Spanning-tree…

A high-performance implementation of an interface for the Spanning-tree Progression Analysis of Density-normalized Events algorithm for tree-based analysis and visualization of this high-dimensional…

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.

SPICE
Desktop

SPICE

A data mining software application that analyzes large FLOWJO data sets from…

A data mining software application that analyzes large FLOWJO data sets from polychromatic flow cytometry and organizes the normalized data graphically.

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