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This is the development version of lemur; for the stable release version, see lemur.

Latent Embedding Multivariate Regression

Bioconductor version: Development (3.20)

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.

Author: Constantin Ahlmann-Eltze [aut, cre]

Maintainer: Constantin Ahlmann-Eltze <artjom31415 at>

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


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biocViews DifferentialExpression, DimensionReduction, Regression, SingleCell, Software, Transcriptomics
Version 1.3.2
In Bioconductor since BioC 3.18 (R-4.3) (0.5 years)
License MIT + file LICENSE
Depends R (>= 4.1)
Imports stats, utils, irlba, methods, SingleCellExperiment, SummarizedExperiment, rlang, vctrs, glmGamPoi(>= 1.12.0), BiocGenerics, S4Vectors, Matrix, DelayedMatrixStats, HDF5Array, MatrixGenerics, matrixStats, Rcpp, harmony (>= 1.0.3), limma, BiocNeighbors
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