Bioinformatics workflow tools | Flow cytometry data analysis
Automation technologies developed during the last several years have enabled the use of flow cytometry (FCM) to generate large, complex data sets in both basic and clinical research applications (Brinkman et al., 2007). A serious bottleneck in the interpretation of existing studies and the application of high throughput FCM to even larger, more complex problems is that data management and data analysis methods have not advanced sufficiently far from the methods developed for applications of FCM to small-scale, tube-based studies . In particular, the data often need to be organized into groups of samples based on combinations of additional covariates and similar operations need to be applied to these groups in a transparent and reproducible manner. Furthermore, the growing depth of knowledge in the field of immunology, for instance the characterization of distinct human T-cell sub-population , clearly argues for more systematic approaches.
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.
Enables flow and image cytometry data analysis. FCS Express RUO is able to analyze flow cytometry data, with flow cytometry tools, plots, and gates. The software allows export to Powerpoint, pdf, Excel, Word, and Microsoft office.
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.
Delivers software packages to facilitate the analysis of Big Data within the field of biology, more specifically immunology. Funky Cells includes several tools for Microsoft Excel including data mining tools for highly multi parametric flow cytometry data (boolean data miner), easy control of pivot tables, heat maps, scatter plots, function tracker, data harmonisation and many other. A special part of the software package is dedicated to the analysis of flow cytometry data based on boolean combination gate analysis. This part includes an analytical platform for cellular polyfunctionality analysis, including the polyfunctionality index algorithm
Enables automated, datadriven gating of high-dimensional flow cytometry (FCM) data sets. OpenCyto is a collection of well-integrated open-source R/BioConductor packages: ncdfFlow, flowCore, flowViz, flowWorkspace, and openCyto. The software aims to meet the challenges of ease of use, interpretability, scalability, collaboration, comparative analysis, reproducibility and robustness, while allowing analysts to integrate domain-specific knowledge into the analysis pipeline. It supports importing gates from external software.
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.