Using coexpression to explore cell-type diversity with the fcoex package

Abstract

Here, we present the fcoex package, which infers coexpression from scRNA-seq data and yields multiple, overlapping classes of cells based on coexpression modules. The tool extends the current scRNA-seq toolbox, providing a multi-hierarchy view on cell functionality and enabling the development of more complete cell atlases. Single-cell RNA sequencing (scRNA-seq) captures details of the cellular landscape, basing a fine-grained view on biological processes. Current pipelines, however, are restricted to single-label perspectives, missing details of the classification landscape. In the pbmc3k blood cell dataset, fcoex detects known classes, like antigen-presenting cells and a new theoretical group of cells, marked by the expression of FCGR3A (CD16). Fcoex extends the current scRNA-seq toolbox, providing a multi-hierarchy view on cell functions as a tool to develop complete cell type atlases. Availability and ImplementationFcoex is written in R and openly available in Bioconductor (https://bioconductor.org/packages/fcoex/). Supplementary informationSupplementary data is available at the end of the manuscript. Source code for analysis is available at https://github.com/csbl-inovausp/fcoex_analysis;