Package: dreamlet
Type: Package
Title: Scalable differential expression analysis of single cell
        transcriptomics datasets with complex study designs
Version: 1.9.0
Date: 2025-04-24
Authors@R: person("Gabriel", "Hoffman", role=c("aut", "cre"), email="gabriel.hoffman@mssm.edu", comment=c(ORCID="0000-0002-0957-0224"))
Description: Recent advances in single cell/nucleus transcriptomic
        technology has enabled collection of cohort-scale datasets to
        study cell type specific gene expression differences associated
        disease state, stimulus, and genetic regulation. The scale of
        these data, complex study designs, and low read count per cell
        mean that characterizing cell type specific molecular
        mechanisms requires a user-frieldly, purpose-build analytical
        framework. We have developed the dreamlet package that applies
        a pseudobulk approach and fits a regression model for each gene
        and cell cluster to test differential expression across
        individuals associated with a trait of interest. Use of
        precision-weighted linear mixed models enables accounting for
        repeated measures study designs, high dimensional batch
        effects, and varying sequencing depth or observed cells per
        biosample.
VignetteBuilder: knitr
License: Artistic-2.0
Encoding: UTF-8
URL: https://DiseaseNeurogenomics.github.io/dreamlet
BugReports: https://github.com/DiseaseNeurogenomics/dreamlet/issues
Suggests: BiocStyle, knitr, pander, rmarkdown, muscat, ExperimentHub,
        RUnit, muscData, scater, scuttle
biocViews: RNASeq, GeneExpression, DifferentialExpression, BatchEffect,
        QualityControl, Regression, GeneSetEnrichment, GeneRegulation,
        Epigenetics, FunctionalGenomics, Transcriptomics,
        Normalization, SingleCell, Preprocessing, Sequencing,
        ImmunoOncology, Software
Depends: R (>= 4.3.0), variancePartition (>= 1.36.1),
        SingleCellExperiment, ggplot2
Imports: edgeR, SummarizedExperiment, DelayedMatrixStats,
        sparseMatrixStats, MatrixGenerics, Matrix, methods, purrr,
        GSEABase, data.table, zenith (>= 1.1.2), mashr (>= 0.2.52),
        ashr, dplyr, BiocParallel, ggbeeswarm, S4Vectors, IRanges,
        irlba, limma, metafor, remaCor, broom, tidyr, rlang,
        BiocGenerics, S4Arrays, SparseArray, DelayedArray, gtools,
        reshape2, ggrepel, scattermore, Rcpp, lme4 (>= 1.1-33), MASS,
        Rdpack, utils, stats
RoxygenNote: 7.3.2
RdMacros: Rdpack
SystemRequirements: C++11
LinkingTo: Rcpp, beachmat
Config/pak/sysreqs: cmake make libicu-dev libpng-dev libxml2-dev
        libssl-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 15:25:03 UTC
RemoteUrl: https://github.com/bioc/dreamlet
RemoteRef: HEAD
RemoteSha: dfc1aac6c48c38b629078309182f6410086e2c3c
NeedsCompilation: yes
Packaged: 2025-10-30 05:32:27 UTC; root
Author: Gabriel Hoffman [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-0957-0224>)
Maintainer: Gabriel Hoffman <gabriel.hoffman@mssm.edu>
Built: R 4.6.0; x86_64-w64-mingw32; 2025-10-30 05:36:32 UTC; windows
Archs: x64
