Package: lemur
Type: Package
Title: Latent Embedding Multivariate Regression
Version: 1.6.1
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
git_url: https://git.bioconductor.org/packages/lemur
git_branch: RELEASE_3_21
git_last_commit: 126bb86
git_last_commit_date: 2025-05-08
Repository: Bioconductor 3.21
Date/Publication: 2025-05-08
NeedsCompilation: yes
Packaged: 2025-05-09 00:17:02 UTC; biocbuild
Author: Constantin Ahlmann-Eltze [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-3762-068X>)
Maintainer: Constantin Ahlmann-Eltze <artjom31415@googlemail.com>
Built: R 4.5.0; x86_64-w64-mingw32; 2025-05-09 13:17:56 UTC; windows
Archs: x64
