Package: muscat 1.19.0

Helena L. Crowell

muscat: Multi-sample multi-group scRNA-seq data analysis tools

`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.

Authors:Helena L. Crowell [aut, cre], Pierre-Luc Germain [aut], Charlotte Soneson [aut], Anthony Sonrel [aut], Mark D. Robinson [aut, fnd]

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muscat.pdf |muscat.html✨
muscat/json (API)
NEWS

# Install 'muscat' in R:

install.packages('muscat', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/helenalc/muscat/issues

Datasets:

example_sce - Example datasets

On BioConductor:muscat-1.19.0(bioc 3.20)muscat-1.18.0(bioc 3.19)

bioconductor-package

11 exports 1.16 score 168 dependencies 4 mentions

Last updated 2 months agofrom:e015e1d950

Exports:aggregateData calcExprFreqs mmDS pbDS pbFlatten pbHeatmap pbMDS prepSCE prepSim resDS simData

Dependencies:abind aod askpass backports beachmat beeswarm BH Biobase BiocGenerics BiocNeighbors BiocParallel BiocSingular bitops blme boot broom Cairo caTools circlize cli clue cluster codetools colorspace ComplexHeatmap corpcor cowplot cpp11 crayon curl data.table DelayedArray DelayedMatrixStats Deriv DESeq2 digest doBy doParallel dplyr dqrng edgeR EnvStats fANCOVA fansi farver FNN foreach formatR futile.logger futile.options future future.apply generics GenomeInfoDb GenomeInfoDbData GenomicRanges GetoptLong ggbeeswarm ggplot2 ggrastr ggrepel glmmTMB GlobalOptions globals glue gplots gridExtra gtable gtools hms httr IRanges irlba isoband iterators jsonlite KernSmooth labeling lambda.r lattice lifecycle limma listenv lme4 lmerTest locfit magrittr MASS Matrix MatrixGenerics matrixStats mgcv microbenchmark mime minqa modelr munsell mvtnorm nlme nloptr nortest numDeriv openssl parallelly pbkrtest pheatmap pillar pkgconfig plyr png prettyunits progress purrr R6 ragg rbibutils RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppHNSW RcppML RcppProgress Rdpack remaCor reshape2 RhpcBLASctl rjson rlang RSpectra rsvd Rtsne S4Arrays S4Vectors ScaledMatrix scales scater sctransform scuttle shape SingleCellExperiment sitmo snow SparseArray sparseMatrixStats statmod stringi stringr SummarizedExperiment sys systemfonts textshaping tibble tidyr tidyselect TMB UCSC.utils utf8 uwot variancePartition vctrs vipor viridis viridisLite withr XVector zlibbioc

Differential state analysis with muscat

Helena L Crowell, Charlotte Soneson, Pierre-Luc Germain, Mark D Robinson

Rendered fromanalysis.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2023-07-26
Started: 2020-02-04

Simulating complex design scRNA-seq data with muscat

Helena L Crowell, Charlotte Soneson, Pierre-Luc Germain, Mark D Robinson

Rendered fromsimulation.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2023-02-09
Started: 2020-02-04

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Aggregation of single-cell to pseudobulk data	aggregateData
calcExprFreqs	calcExprFreqs
Example datasets	data example_sce
DS analysis using mixed-models (MM)	.mm_dream .mm_dream2 .mm_glmm .mm_vst mmDS
pseudobulk DS analysis	pbDS
pbFlatten Flatten pseudobulk SCE	pbFlatten
Heatmap of cluster-sample pseudobulks	pbHeatmap
Pseudobulk-level MDS plot	pbMDS
Prepare SCE for DS analysis	prepSCE
SCE preparation for 'simData'	prepSim
resDS Formatting of DS analysis results	resDS
simData	simData