lemur
This is thereleased version of lemur; for the devel version, seelemur.
Latent Embedding Multivariate Regression
Bioconductor version: Release (3.22)
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: 0000-0002-3762-068X
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")BiocManager::install("lemur")For older versions of R, please refer to the appropriateBioconductor 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 | 1.8.0 |
| In Bioconductor since | BioC 3.18 (R-4.3) (2 years) |
| License | MIT + fileLICENSE |
| 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
FollowInstallation instructions to use this package in your R session.
| Source Package | lemur_1.8.0.tar.gz |
| Windows Binary (x86_64) | lemur_1.8.0.zip |
| macOS Binary (x86_64) | lemur_1.8.0.tgz |
| macOS Binary (arm64) | lemur_1.8.0.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 |