Package: lemur 1.11.2

Constantin Ahlmann-Eltze

lemur: Latent Embedding Multivariate Regression

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.

Authors:Constantin Ahlmann-Eltze [aut, cre]

lemur_1.11.2.tar.gz
lemur_1.11.2.zip(r-4.7)lemur_1.11.2.zip(r-4.6)lemur_1.11.2.zip(r-4.5)
lemur_1.11.2.tgz(r-4.6-x86_64)lemur_1.11.2.tgz(r-4.6-arm64)lemur_1.11.2.tgz(r-4.5-x86_64)lemur_1.11.2.tgz(r-4.5-arm64)
lemur_1.11.2.tar.gz(r-4.7-arm64)lemur_1.11.2.tar.gz(r-4.7-x86_64)lemur_1.11.2.tar.gz(r-4.6-arm64)lemur_1.11.2.tar.gz(r-4.6-x86_64)
lemur_1.11.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
lemur/json (API)

# Install 'lemur' in R:

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

Bug tracker:https://github.com/const-ae/lemur/issues

Uses libs:

openblas– Optimized BLAS
c++– GNU Standard C++ Library v3

Datasets:

glioblastoma_example_data - The 'glioblastoma_example_data' dataset

On BioConductor:lemur-1.11.1(bioc 3.24)lemur-1.9.0(bioc 3.23)

transcriptomics differentialexpression singlecell dimensionreduction regression quarto openblas cpp

8.09 score 102 stars 121 scripts 328 downloads 11 exports 42 dependencies

Last updated from:086bf8b842. Checks:9 WARNING, 3 ERROR, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	222
linux-devel-arm64	ERROR	333
linux-devel-x86_64	ERROR	430
source / vignettes	OK	371
linux-release-arm64	WARNING	337
linux-release-x86_64	WARNING	460
macos-release-arm64	WARNING	236
macos-release-x86_64	WARNING	682
macos-oldrel-arm64	WARNING	228
macos-oldrel-x86_64	WARNING	369
windows-devel	ERROR	364
windows-release	WARNING	389
windows-oldrel	WARNING	340
wasm-release	OK	182

Exports:.lemur_fit align_by_grouping align_harmony compute_contrasts design find_de_neighborhoods lemur project_on_lemur_fit residuals test_de vars

Dependencies:abind assorthead beachmat Biobase BiocGenerics biocmake BiocNeighbors cli DelayedArray DelayedMatrixStats dir.expiry filelock generics GenomicRanges glmGamPoi glue h5mread HDF5Array IRanges irlba lattice lifecycle limma Matrix MatrixGenerics matrixStats Rcpp RcppArmadillo rhdf5 rhdf5filters Rhdf5lib rlang S4Arrays S4Vectors Seqinfo SingleCellExperiment SparseArray sparseMatrixStats statmod SummarizedExperiment vctrs XVector

Introduction

Latent Embedding Multivariate Regression (LEMUR) | Installation | A note to users | Overview | A worked through example | Using cell type annotation | FAQ | I have already integrated my data using Harmony / MNN / Seurat. Can I call lemur directly with the aligned data? | Can I call lemur with sctransformed instead of log-transformed data? | My data appears less integrated after calling lemur than before. What is happening?! | The conditions still separate if I plot the data using UMAP / t-SNE, even after calling align_harmony / align_neighbors. What should I do? | How do I make lemur faster? | Session Info

Rendered fromIntroduction.qmdusingquarto::html

Last update: 2026-03-20
Started: 2026-02-18

Help page	Topics
Access values from a 'lemur_fit'	$,lemur_fit-method $<-,lemur_fit-method .DollarNames.lemur_fit dollar_methods
Enforce additional alignment of cell clusters beyond the direct differential embedding	align_by_grouping align_harmony
Predict log fold changes between conditions for each cell. Both names 'compute_contrasts' and 'test_de' bind to the same function, but the former is more evocative.	compute_contrasts test_de
Find differential expression neighborhoods	find_de_neighborhoods
The 'glioblastoma_example_data' dataset	glioblastoma_example_data
Main function to fit the latent embedding multivariate regression (LEMUR) model	lemur
The 'lemur_fit' class	.lemur_fit design,lemur_fit-method lemur_fit lemur_fit-class [,lemur_fit,ANY,ANY,ANY-method
Predict values from 'lemur_fit' object	predict.lemur_fit
Project new data onto the latent spaces of an existing lemur fit	project_on_lemur_fit
Predict values from 'lemur_fit' object	residuals,lemur_fit-method
Differential embedding for each condition	test_global

Package: lemur 1.11.2

lemur: Latent Embedding Multivariate Regression

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)