SPIRAL: Significant Process InfeRence ALgorithm for single cell RNA-sequencing and spatial transcriptomics

1 Gene expression data is complex and may hold information regarding multiple biological processes at once. We present SPIRAL, an algorithm that uses a Gaussian statistical model to produce a comprehensive overview of a plurality of significant processes detected in single cell RNA-seq or spatial transcriptomics data. SPIRAL identifies biological processes by finding sub-matrices that consist of the subset of genes involved and the subset of cells or spots. We describe the algorithmic method, the analysis pipeline and several example results. SPIRAL is available at https://spiral.technion.ac.il/ .