scBio

The software tool "scBio" introduces the Cell Population Mapping (CPM) algorithm, a method for the analysis of single-cell RNA sequencing (scRNA-seq) data. scRNA-seq is a technique that uncovers the diversity of cell types and states within complex tissues, highlighting the cellular heterogeneity critical for understanding biological processes and disease mechanisms. The CPM algorithm, embedded within the scBio package available on CRAN (a repository for R packages), utilizes reference scRNA-seq profiles to deconvolve bulk transcriptome data. This approach allows researchers to infer the composition of cell types and states in a sample, providing insights into the cellular architecture of tissues without the need for single-cell resolution data.

The utility of scBio and its CPM algorithm is exemplified through its application in studying the lungs of mice infected with the influenza virus. This analysis uncovered that the relationship between the abundance of specific cell types (or states) and the clinical symptoms of influenza is a property specific to the cell state. Moreover, this relationship varies along a continuum of cell activation states, indicating a gradational change rather than a binary or abrupt transition between states. Subsequent experiments and mathematical modeling confirmed these findings, demonstrating the gradual dynamics of cell-state changes in clinical outcomes of influenza infection.