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 (3.24)
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] 
Maintainer: Gabriel Hoffman <gabriel.hoffman at mssm.edu>
citation("dreamlet")):Gabriel Hoffman. dreamlet: Scalable differential expression analysis of single cell transcriptomics datasets with complex study designs. doi:10.18129/B9.bioc.dreamlet, R package version 1.11.0, https://bioconductor.org/packages/dreamlet.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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")| Modeling continuous cell-level covariates | HTML | R Script |
| Dreamlet analysis of single cell RNA-seq | HTML | R Script |
| Error handling | HTML | R Script |
| Loading large-scale H5AD datasets | HTML | R Script |
| mashr analysis following dreamlet | HTML | |
| Testing non-linear effects | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BatchEffect, DifferentialExpression, Epigenetics, FunctionalGenomics, GeneExpression, GeneRegulation, GeneSetEnrichment, ImmunoOncology, Normalization, Preprocessing, QualityControl, RNASeq, Regression, Sequencing, SingleCell, Software, Transcriptomics |
| Version | 1.11.0 |
| In Bioconductor since | BioC 3.18 (R-4.3) (3 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, reformulas, BiocParallel, ggbeeswarm, S4Vectors, IRanges, irlba, limma, metafor, remaCor, broom, tidyr, rlang, BiocGenerics, S4Arrays, SparseArray, DelayedArray, gtools, reshape2, ggrepel, scattermore, Rcpp, 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, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | dreamlet_1.11.0.tar.gz |
| Windows Binary (x86_64) | dreamlet_1.11.0.zip |
| macOS Binary (big-sur-x86_64) | dreamlet_1.11.0.tgz |
| macOS Binary (sonoma-arm64) | dreamlet_1.11.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/dreamlet |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/dreamlet |
| Package Short Url | https://bioconductor.org/packages/dreamlet/ |
| Package Downloads Report | Download Stats |