{ "_id": "6a1ae1911d7bb097a09eda0e", "Package": "dreamlet", "Type": "Package", "Title": "Scalable differential expression analysis of single cell\ntranscriptomics datasets with complex study designs", "Version": "1.11.0", "Date": "2026-04-13", "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\ntechnology has enabled collection of cohort-scale datasets to\nstudy cell type specific gene expression differences associated\ndisease state, stimulus, and genetic regulation. The scale of\nthese data, complex study designs, and low read count per cell\nmean that characterizing cell type specific molecular\nmechanisms requires a user-frieldly, purpose-build analytical\nframework. We have developed the dreamlet package that applies\na pseudobulk approach and fits a regression model for each gene\nand cell cluster to test differential expression across\nindividuals associated with a trait of interest. Use of\nprecision-weighted linear mixed models enables accounting for\nrepeated measures study designs, high dimensional batch\neffects, and varying sequencing depth or observed cells per\nbiosample.", "VignetteBuilder": "knitr", "License": "Artistic-2.0", "Encoding": "UTF-8", "URL": "https://DiseaseNeurogenomics.github.io/dreamlet", "BugReports": "https://github.com/DiseaseNeurogenomics/dreamlet/issues", "biocViews": "RNASeq, GeneExpression, DifferentialExpression, BatchEffect,\nQualityControl, Regression, GeneSetEnrichment, GeneRegulation,\nEpigenetics, FunctionalGenomics, Transcriptomics,\nNormalization, SingleCell, Preprocessing, Sequencing,\nImmunoOncology, Software", "RoxygenNote": "7.3.3", "RdMacros": "Rdpack", "SystemRequirements": "C++11", "Config/pak/sysreqs": "cmake make libicu-dev libpng-dev libxml2-dev\nlibssl-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 13:01:27 UTC", "RemoteUrl": "https://github.com/bioc/dreamlet", 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