Data preprocessing software tools | Flow cytometry analysis
The rapid growth in the multidimensionality and throughput of flow cytometry data, particularly in the 2000s, has led to the creation of a variety of computational analysis methods, data standards, and public databases for the sharing of results. Computational methods exist to assist in the preprocessing of flow cytometry data, identifying cell populations within it, matching those cell populations across samples, and performing diagnosis and discovery using the results of previous steps. For preprocessing, this includes compensating for spectral overlap, transforming data onto scales conducive to visualization and analysis, assessing data for quality, and normalizing data across samples and experiments.
A data management system for flow cytometry data analysis. flowCore allows to handle flow cytometry high content screening data and encourages open development of tools for their coherent analysis. A key component of this package is having suitable data structures that support the application of similar operations to a collection of samples or a clinical cohort. Flowcore constitutes a shared and extensible research platform that enables collaboration between bioinformaticians, statisticians, biologists and clinicians.
Offers access to over 180 tools for the analysis of gene expression (RNA-seq and microarray), sequence variation and copy number, proteomic, flow cytometry, and network analysis. GenePattern is a genomic analysis platform that provides tools in the form of modules. Users can submit their data and choose suitable settings for performing complex analyses without detailed knowledge of the underlying programming language, algorithms and settings.
Offers a platform dedicated to cytometry analysis. WinList is an application provindingg a wide range of features including: (i) the production of ratio parameters, equations, alerts as well as reusable report templates and individual histograms; (ii) multiple analysis dealing with rare-event or leukemia-lymphomaanalysis; (iii) the highlighting of events and possible relationships of markers.
Assists in the reading, processing, analysis, and visualization of data from 96-well plates, specifically data from the different COPAS platforms. COPASutils can read, summarize, and clean data to present graphical and adaptable visualizations of both summary and distribution statistics. It employs a support vector machine (SVM) to probabilistically determine if an object recorded by the COPAS software is an undesirable bubble or a true object to be measured. This tool is able to reduce the number of false objects analyzed.
Provides a way to extract data from one such commercial package, FlowJo, into the publicly accessible analysis platform R/Bioconductor. flowflowJo can produce R data structures with either summary statistics or fully flowCore compliant objects representing the various gates, compensation matrices, and other related information embedded in FlowJo sessions. Its goal is to make it easy to use compensation and gating information that has been produced using FlowJo. The flowFlowJo package provides the ability to work with both the raw data and the gating information in a powerful analysis environment that makes full use of the existing open source community efforts. Additional functionality is gained by the ability of the user to effectively run all of the compensation and gating functions described by the workspace(s) and automatically retrieve all of the relevant summary statistics into a concise data structure.
Assists users in flow cytometry analyzing. ModFit LT is a standalone software including features for (i) investigating data with perturbed populations; (ii) detecting peaks; (iii) identifying ploidy patterns of a sample; (iv) performing cell tracking dye samples; (v) studying cell proliferation. The software is also able to generate multiple customized reports that can be used as templates coupled to additional functions for exporting.