lemur
This is the development version of lemur; for the stable release version, see lemur.
Latent Embedding Multivariate Regression
Bioconductor version: Development (3.21)
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] (ORCID:
Maintainer: Constantin Ahlmann-Eltze <artjom31415 at googlemail.com>
citation("lemur")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("lemur")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("lemur")| Introduction | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DifferentialExpression, DimensionReduction, Regression, SingleCell, Software, Transcriptomics |
| Version | 1.5.0 |
| In Bioconductor since | BioC 3.18 (R-4.3) (1 year) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.1) |
| 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 |
| System Requirements | |
| URL | https://github.com/const-ae/lemur |
| Bug Reports | https://github.com/const-ae/lemur/issues |
See More
| Suggests | testthat (>= 3.0.0), tidyverse, uwot, dplyr, edgeR, knitr, rmarkdown, BiocStyle |
| Linking To | Rcpp, RcppArmadillo |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | lemur_1.5.0.tar.gz |
| Windows Binary (x86_64) | |
| 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 |