Welcome to the new bioconductor.org!

lemur

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

Latent Embedding Multivariate Regression


Bioconductor version: Development (3.19)

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 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")

# 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 PDF
NEWS Text
LICENSE Text

Details

biocViews DifferentialExpression, DimensionReduction, Regression, SingleCell, Software, Transcriptomics
Version 1.1.6
In Bioconductor since BioC 3.18 (R-4.3) (< 6 months)
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, 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_1.1.6.tar.gz
Windows Binary lemur_1.1.6.zip
macOS Binary (x86_64) lemur_1.1.6.tgz
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