spane2

Spane2 is a software tool designed for the analysis and visualization of single-cell RNA sequencing (scRNA-seq) data. It is part of the Spane suite of tools, which are developed by the Computational Biology Group at the University of Cambridge.

The primary function of Spane2 is to identify and visualize cell populations within scRNA-seq datasets. It uses dimensionality reduction techniques, such as t-distributed stochastic neighbor embedding (t-SNE) and uniform manifold approximation and projection (UMAP), to map high-dimensional gene expression data into two or three dimensions. This allows researchers to visually inspect the data and identify distinct clusters of cells that correspond to different cell types or states.

Spane2 also provides tools for differential expression analysis, allowing researchers to identify genes that are differentially expressed between different cell populations. This can help in understanding the molecular basis of cell differentiation and the regulation of gene expression.

One of the key features of Spane2 is its integration with other bioinformatics tools, such as Seurat and Scanpy. This allows researchers to seamlessly incorporate Spane2 into their existing workflows and take advantage of the complementary strengths of different tools.

Spane2 is an open-source software, released under the GNU General Public License. It is available for download from the Spane website, and the source code is available on GitHub. The software is supported by an active user community, and regular updates are provided to address user feedback and incorporate new features.

Overall, Spane2 is a powerful tool for the analysis and visualization of scRNA-seq data, providing researchers with the means to gain insights into the complexity of single-cell transcriptomes.