FlowsContigt

FlowsContigt is a computational tool designed for analyzing and visualizing flow cytometry data, particularly in the context of single-cell analysis. It is part of the broader suite of tools developed for handling high-dimensional biological data, often used in conjunction with other bioinformatics pipelines. The software is particularly useful for identifying and characterizing cell populations based on their phenotypic properties, such as surface markers or intracellular proteins.

Developed as an open-source solution, FlowsContigt leverages clustering algorithms to group similar cell events into discrete populations. This is achieved through dimensionality reduction techniques, such as t-distributed stochastic neighbor embedding (t-SNE) or uniform manifold approximation and projection (UMAP), followed by contour-based segmentation. The tool allows researchers to visualize complex flow cytometry datasets in two or three dimensions, making it easier to interpret high-dimensional data.

FlowsContigt is often integrated into workflows that involve preprocessing raw flow cytometry data, such as gating and compensation, before applying clustering methods. It is compatible with standard flow cytometry file formats, including FCS (Flow Cytometry Standard) files, and can be used alongside other bioinformatics tools for downstream analysis, such as differential expression analysis or trajectory inference.

The software is designed to be user-friendly, offering both command-line and graphical interfaces for users with varying levels of technical expertise. It is widely used in immunology, cancer research, and stem cell biology, where single-cell resolution is critical for understanding cellular heterogeneity and function. While FlowsContigt itself does not perform statistical testing, it provides a foundation for further analysis by enabling precise population identification, which can then be subjected to more advanced statistical methods.