Package: exposomeSC
Title: Single-Cell Exposome-Wide Association Studies with Cross-Omic
        Network Inference
Version: 0.99.1
Authors@R: 
    person(given = "Cuiwei",
           family = "Gao",
           email = "48gaocuiwei@gmail.com",
           role = c("aut", "cre"))
Description: 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.
License: Artistic-2.0
Depends: R (>= 4.5.0)
Imports: methods, Matrix, S4Vectors (>= 0.32.0), SummarizedExperiment,
        SingleCellExperiment, stats, BiocParallel, MASS, edgeR (>=
        4.0.0), limma, withr
Suggests: DESeq2, variancePartition, fgsea, lme4, lmerTest, pbkrtest,
        mgcv, qgcomp, mediation, glasso, Biobase, SpatialExperiment,
        coglasso, igraph, ggraph, tidygraph, ggplot2, metafor, ppcor,
        statmod, testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle,
        BiocCheck
Config/testthat/edition: 3
biocViews: SingleCell, GeneExpression, DifferentialExpression,
        Transcriptomics, CellBiology, StatisticalMethod, Network,
        NetworkInference, Regression
URL: https://github.com/CuiweiG/exposomeSC
BugReports: https://github.com/CuiweiG/exposomeSC/issues
Encoding: UTF-8
RoxygenNote: 7.3.3
VignetteBuilder: knitr
Collate: 'AllClasses.R' 'AllGenerics.R' 'below-lod.R' 'build-scee.R'
        'bridge.R' 'utils.R' 'causal-mediation.R' 'cell-coupling.R'
        'composition.R' 'data-docs.R' 'dose-response.R' 'enrichment.R'
        'erd-interventional.R' 'exposomeSC-package.R' 'gam-dr.R'
        'glmm-inference.R' 'iers.R' 'interaction.R' 'mediation.R'
        'meta-analysis.R' 'methods.R' 'mixture.R' 'sc-exwas.R'
        'multi-exwas.R' 'network-utils.R' 'network-build.R'
        'network-compare.R' 'network-differential.R'
        'network-mediation.R' 'network-plots.R' 'network-simulate.R'
        'network-temporal.R' 'power.R' 'qgcomp-mixture.R' 'spatial.R'
        'state-coupling.R'
Config/pak/sysreqs: zlib1g-dev
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-09-23 11:56:39 UTC
RemoteUrl: https://github.com/BiocStaging/exposomeSC
RemoteRef: HEAD
RemoteSha: 349221639c2f7d246a61c527939db1e69c58d5d4
NeedsCompilation: no
Packaged: 2026-09-23 17:24:14 UTC; root
Author: Cuiwei Gao [aut, cre]
Maintainer: Cuiwei Gao <48gaocuiwei@gmail.com>