lemur
Latent Embedding Multivariate Regression
Bioconductor version: 3.24 · Package version: 1.11.2
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
Fit a latent embedding multivariate regression (LEMUR) model to multi-condition single-cell data. The model provides a parametric description of single-cell data measured with treatment vs. control or more complex experimental designs. The parametric model is used to (1) align conditions, (2) predict log fold changes between conditions for all cells, and (3) identify cell neighborhoods with consistent log fold changes. For those neighborhoods, a pseudobulked differential expression test is conducted to assess which genes are significantly changed.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("lemur")Details
| Maintainer | Constantin Ahlmann-Eltze <artjom31415@googlemail.com> |
| Author | Constantin Ahlmann-Eltze [aut, cre] (ORCID: <https://orcid.org/0000-0002-3762-068X>) |
| License | MIT + file LICENSE |
| URL | https://github.com/const-ae/lemur |
| Bug Reports | https://github.com/const-ae/lemur/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | DifferentialExpression, DimensionReduction, Regression, SingleCell, Software, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/lemur/ |
Citation
From within R, enter citation("lemur"):
Constantin Ahlmann-Eltze. lemur: Latent Embedding Multivariate Regression. doi:10.18129/B9.bioc.lemur, R package version 1.11.2, https://bioconductor.org/packages/lemur.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | lemur_1.11.2.tar.gz |
| Windows binary (x86_64) | lemur_1.11.2.zip |
| macOS binary (arm64) | lemur_1.11.2.tgz |
| macOS binary (x86_64) | lemur_1.11.2.tgz |
Dependencies
Depends: R (>= 4.1)
Imports: stats, utils, irlba, methods, SingleCellExperiment, SummarizedExperiment, rlang (>= 1.1.0), vctrs (>= 0.6.0), glmGamPoi (>= 1.12.0), BiocGenerics, S4Vectors, Matrix, DelayedMatrixStats, HDF5Array, MatrixGenerics, matrixStats, Rcpp, limma, BiocNeighbors
LinkingTo: Rcpp, RcppArmadillo
Suggests: testthat (>= 3.0.0), tidyverse, uwot, dplyr, edgeR, knitr, quarto, BiocStyle