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Bioconductor - dreamlet (development version)

dreamlet

This is the development version of dreamlet; for the stable release version, see dreamlet.

Scalable differential expression analysis of single cell transcriptomics datasets with complex study designs

Bioconductor version: Development (3.22)

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.

Author: Gabriel Hoffman [aut, cre] ORCID: 0000-0002-0957-0224

Maintainer: Gabriel Hoffman <gabriel.hoffman at mssm.edu>

Citation (from within R, enter citation("dreamlet")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("dreamlet")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("dreamlet")

Details biocViews BatchEffect, DifferentialExpression, Epigenetics, FunctionalGenomics, GeneExpression, GeneRegulation, GeneSetEnrichment, ImmunoOncology, Normalization, Preprocessing, QualityControl, RNASeq, Regression, Sequencing, SingleCell, Software, Transcriptomics Version 1.7.1 In Bioconductor since BioC 3.18 (R-4.3) (1.5 years) License Artistic-2.0 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 System Requirements C++11 URL https://DiseaseNeurogenomics.github.io/dreamlet Bug Reports https://github.com/DiseaseNeurogenomics/dreamlet/issues See More Suggests BiocStyle, knitr, pander, rmarkdown, muscat, ExperimentHub, RUnit, muscData, scater, scuttle Linking To Rcpp, beachmat Enhances Depends On Me Imports Me Suggests Me crumblr Links To Me Build Report Build Report Package Archives

Follow Installation instructions to use this package in your R session.

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