Package: lemur
Type: Package
Title: Latent Embedding Multivariate Regression
Version: 1.9.0
Authors@R: person("Constantin", "Ahlmann-Eltze", email = "artjom31415@googlemail.com", 
               role = c("aut", "cre"), comment = c(ORCID = "0000-0002-3762-068X"))
Description: 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.
URL: https://github.com/const-ae/lemur
BugReports: https://github.com/const-ae/lemur/issues
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: false
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, harmony (>= 1.2.0), limma, BiocNeighbors
Suggests: testthat (>= 3.0.0), tidyverse, uwot, dplyr, edgeR, knitr,
        rmarkdown, BiocStyle
LinkingTo: Rcpp, RcppArmadillo
Depends: R (>= 4.1)
Config/testthat/edition: 3
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
biocViews: Transcriptomics, DifferentialExpression, SingleCell,
        DimensionReduction, Regression
VignetteBuilder: knitr
Config/pak/sysreqs: libssl-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 15:26:19 UTC
RemoteUrl: https://github.com/bioc/lemur
RemoteRef: HEAD
RemoteSha: 2426da61746c61e1537dffc769251085766bf297
NeedsCompilation: yes
Packaged: 2026-01-09 21:28:30 UTC; root
Author: Constantin Ahlmann-Eltze [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-3762-068X>)
Maintainer: Constantin Ahlmann-Eltze <artjom31415@googlemail.com>
Built: R 4.6.0; x86_64-apple-darwin20; 2026-01-09 22:15:34 UTC; unix
