lemur

This is the released version of lemur; for the devel version, see lemur.

Latent Embedding Multivariate Regression

Bioconductor version: Release (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 googlemail.com>

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

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

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	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DifferentialExpression, DimensionReduction, Regression, SingleCell, Software, Transcriptomics
Version	1.4.0
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

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_1.4.0.tar.gz
Windows Binary (x86_64)	lemur_1.4.0.zip
macOS Binary (x86_64)	lemur_1.4.0.tgz
macOS Binary (arm64)	lemur_1.4.0.tgz
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