muscat
Multi-sample multi-group scRNA-seq data analysis tools
Bioconductor version: 3.23 · Package version: 1.26.0
`muscat` provides various methods and visualization tools for DS analysis in multi-sample, multi-group, multi-(cell-)subpopulation scRNA-seq data, including cell-level mixed models and methods based on aggregated “pseudobulk” data, as well as a flexible simulation platform that mimics both single and multi-sample scRNA-seq data.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("muscat")Details
| Maintainer | Helena L. Crowell <helena@crowell.eu> |
| Author | Helena L. Crowell [aut, cre] (ORCID: <https://orcid.org/0000-0002-4801-1767>), Pierre-Luc Germain [aut], Charlotte Soneson [aut], Anthony Sonrel [aut], Jeroen Gilis [aut], Davide Risso [aut], Lieven Clement [aut], Mark D. Robinson [aut, fnd] |
| License | GPL-3 |
| URL | https://github.com/HelenaLC/muscat |
| Bug Reports | https://github.com/HelenaLC/muscat/issues |
| Downloads rank | 1171 |
| Source branch | RELEASE_3_23 |
| biocViews | DifferentialExpression, ImmunoOncology, Sequencing, SingleCell, Software, StatisticalMethod, Visualization |
Documentation
- Differential state analysis with muscat
- Simulating complex design scRNA-seq data with muscat
- Differential detection analysis
- Increasing power with bulk-based hypothesis weighing (bbhw)
Download
Dependencies
Depends: R (>= 4.5)
Imports: BiocParallel, blme, ComplexHeatmap, dplyr, edgeR, ggplot2, glmmTMB, grDevices, grid, limma, lmerTest, lme4, Matrix, MatrixGenerics, matrixStats, methods, progress, rlang, S4Vectors, scales, scater, scuttle, stats, SingleCellExperiment, SummarizedExperiment, variancePartition
Suggests: BiocStyle, countsimQC, DESeq2, AnnotationHub, ExperimentHub, iCOBRA, IHW, knitr, patchwork, phylogram, RColorBrewer, reshape2, rmarkdown, sctransform, statmod, stageR, testthat, tidyr, UpSetR
Reverse dependencies
Suggests Me (4): crumblr, DeeDeeExperiment, dreamlet, muscData