Package: nebula 1.5.4

nebula: Negative Binomial Mixed Models Using Large-Sample Approximation for Differential Expression Analysis of ScRNA-Seq Data

A fast negative binomial mixed model for conducting association analysis of multi-subject single-cell data. It can be used for identifying marker genes, differential expression and co-expression analyses. The model includes subject-level random effects to account for the hierarchical structure in multi-subject single-cell data. See He et al. (2021) <doi:10.1038/s42003-021-02146-6>.

Authors:Liang He [aut, cre], Raghav Sharma [ctb]

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nebula.pdf |nebula.html✨
nebula/json (API)

# Install 'nebula' in R:

install.packages('nebula', repos = c('https://lhe17.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/lhe17/nebula/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

sample_data - An example data set for testing nebula
sample_seurat - An example data set for testing scToNeb

On CRAN:

cpp

6.43 score 37 stars 145 scripts 219 downloads 4 exports 171 dependencies

Last updated 7 days agofrom:08eb9c1e17. Checks:1 OK, 11 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 26 2025
R-4.5-win-x86_64	NOTE	Mar 26 2025
R-4.5-mac-x86_64	NOTE	Mar 26 2025
R-4.5-mac-aarch64	NOTE	Mar 26 2025
R-4.5-linux-x86_64	NOTE	Mar 26 2025
R-4.4-win-x86_64	NOTE	Mar 26 2025
R-4.4-mac-x86_64	NOTE	Mar 26 2025
R-4.4-mac-aarch64	NOTE	Mar 26 2025
R-4.4-linux-x86_64	NOTE	Mar 26 2025
R-4.3-win-x86_64	NOTE	Mar 26 2025
R-4.3-mac-x86_64	NOTE	Mar 26 2025
R-4.3-mac-aarch64	NOTE	Mar 26 2025

Exports:group_cell nbresidual nebula scToNeb

Dependencies:abind askpass base64enc BH Biobase BiocGenerics bitops bslib cachem caTools cli cluster codetools colorspace commonmark cowplot cpp11 crayon crosstalk curl data.table DelayedArray deldir digest doFuture doRNG dotCall64 dplyr dqrng evaluate fansi farver fastDummies fastmap fitdistrplus FNN fontawesome foreach fs future future.apply generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 ggrepel ggridges globals glue goftest gplots gridExtra gtable gtools here highr htmltools htmlwidgets httpuv httr ica igraph IRanges irlba isoband iterators jquerylib jsonlite KernSmooth knitr labeling later lattice lazyeval leidenbase lifecycle listenv lmtest magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime miniUI munsell nlme nloptr openssl parallelly patchwork pbapply pillar pkgconfig plotly plyr png polyclip progressr promises purrr R6 RANN rappdirs RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppHNSW RcppParallel RcppProgress RcppTOML reshape2 reticulate Rfast rlang rmarkdown rngtools ROCR rprojroot RSpectra Rtsne S4Arrays S4Vectors sass scales scattermore sctransform Seurat SeuratObject shiny SingleCellExperiment sitmo sourcetools sp spam SparseArray spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.univar spatstat.utils stringi stringr SummarizedExperiment survival sys tensor tibble tidyr tidyselect tinytex trust UCSC.utils utf8 uwot vctrs viridisLite withr xfun xtable XVector yaml zigg zoo

A fast negative binomial mixed model for analyzing multi-subject single-cell data

Liang He

Rendered fromnebula_example.Rmdusingknitr::rmarkdownon Mar 26 2025.

Last update: 2025-03-26
Started: 2020-09-23

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Negative Binomial Mixed Models Using Large-Sample Approximation for Differential Expression Analysis of ScRNA-Seq Data	nebula-package
Group cells according to subject IDs	group_cell
Extract Pearson residuals from the results of NEBULA	nbresidual
Association analysis of a multi-subject single-cell data set using a fast negative binomial mixed model	nebula
An example data set for testing nebula	sample_data
An example data set for testing scToNeb	sample_seurat
Retrieve data from Seurat or SingleCellExperiment object to prepare for use in nebula	scToNeb