Package: exposomeSC 0.99.1

exposomeSC: Single-Cell Exposome-Wide Association Studies with Cross-Omic Network Inference

A framework for cell-type-specific exposome-wide association studies (sc-ExWAS) that bridges donor-level environmental exposures with single-cell resolution gene expression. The package extends SingleCellExperiment to store exposure measurements alongside transcriptomic data, and implements donor-level raw-count pseudobulk inference to avoid cellular pseudoreplication (Squair et al. 2021 <doi:10.1038/s41467-021-25960-2>). The default workflow uses robust edgeR quasi-likelihood models, exposure-independent expression-support filtering, complete-transcriptome offsets, design-rank diagnostics, and global multiplicity correction. Additional modules support dose-response modelling, exposure mixtures, cross-cohort synthesis, and cell-level gene-protein coupling. Exploratory decomposition and mediation utilities report model-based associations; they do not by themselves identify causal effects.

Authors:Cuiwei Gao [aut, cre]