lemur

DOI: 10.18129/B9.bioc.lemur  

Latent Embedding Multivariate Regression

Bioconductor version: Release (3.18)

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>

Installation

To install this package, start R (version "4.3") 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")

 

HTML	R Script	Introduction
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	DifferentialExpression, DimensionReduction, Regression, SingleCell, Software, Transcriptomics
Version	1.0.4
In Bioconductor since	BioC 3.18 (R-4.3) (< 6 months)
License	MIT + file LICENSE
Depends	R (>= 4.3)
Imports	stats, utils, irlba, methods, SingleCellExperiment, SummarizedExperiment, rlang, vctrs, glmGamPoi(>= 1.12.0), BiocGenerics, S4Vectors, Matrix, DelayedMatrixStats, HDF5Array, MatrixGenerics, matrixStats, Rcpp, harmony, limma, BiocNeighbors
LinkingTo	Rcpp, RcppArmadillo
Suggests	testthat (>= 3.0.0), tidyverse, uwot, dplyr, edgeR, knitr, rmarkdown, BiocStyle
SystemRequirements
Enhances
URL	https://github.com/const-ae/lemur
BugReports	https://github.com/const-ae/lemur/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	lemur_1.0.4.tar.gz
Windows Binary
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
Old Source Packages for BioC 3.18	Source Archive