DOI: 10.18129/B9.bioc.lemur  

Latent Embedding Multivariate Regression

Bioconductor version: Release (3.18)

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 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.

Author: Constantin Ahlmann-Eltze [aut, cre]

Maintainer: Constantin Ahlmann-Eltze <artjom31415 at googlemail.com>

Citation (from within R, enter citation("lemur")):


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



HTML R Script Introduction
PDF   Reference Manual
Text   NEWS


biocViews DifferentialExpression, DimensionReduction, Regression, SingleCell, Software, Transcriptomics
Version 1.0.4
In Bioconductor since BioC 3.18 (R-4.3) (< 6 months)
License MIT + file LICENSE
Depends R (>= 4.3)
Imports stats, utils, irlba, methods, SingleCellExperiment, SummarizedExperiment, rlang, vctrs, glmGamPoi(>= 1.12.0), BiocGenerics, S4Vectors, Matrix, DelayedMatrixStats, HDF5Array, MatrixGenerics, matrixStats, Rcpp, harmony, limma, BiocNeighbors
LinkingTo Rcpp, RcppArmadillo
Suggests testthat (>= 3.0.0), tidyverse, uwot, dplyr, edgeR, knitr, rmarkdown, BiocStyle
URL https://github.com/const-ae/lemur
BugReports https://github.com/const-ae/lemur/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package lemur_1.0.4.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/lemur
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/lemur
Bioc Package Browser https://code.bioconductor.org/browse/lemur/
Package Short Url https://bioconductor.org/packages/lemur/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.18 Source Archive

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: