Bioinformatics pipeline tools | Flow cytometry analysis

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 [2]. 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 [3], clearly argues for more systematic approaches.

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FCS Express

(1)

Enables flow and image cytometry data analysis. FCS Express 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.

FlowJo

(1)

A flow cytometry data analysis software.. FlowJo contains a list of loaded samples (experimental data), statistics, gates, and other analyses, as well as tabular and graphical layouts. FlowJo provides features and tools for the creation of histogram and other plot overlays, cell cycle analysis, calcium flux analysis, proliferation analysis, quantitation, cluster identification and backgating display.

Funky Cells

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

flowPhyto

An R package that performs aggregate statistics on virtually unlimited collections of raw flow cytometry files and provides a memory efficient, parallelized solution for analyzing high-throughput flow cytometric data.

OpenCyto

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.

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