Package: lemur 1.11.1

Constantin Ahlmann-Eltze

lemur: Latent Embedding Multivariate Regression

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.

Authors:Constantin Ahlmann-Eltze [aut, cre]

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manual.pdf |manual.html✨
card.svg |card.png
lemur/json (API)
NEWS

# Install 'lemur' in R:
install.packages('lemur', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/const-ae/lemur/issues

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
Datasets:

On BioConductor:lemur-1.11.0(bioc 3.24)lemur-1.9.0(bioc 3.23)

transcriptomicsdifferentialexpressionsinglecelldimensionreductionregressionquartoopenblascpp

6.87 score 101 stars 92 scripts 355 downloads 11 exports 65 dependencies

Last updated from:376f2f9130. Checks:1 WARNING, 12 ERROR, 1 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING205
linux-devel-arm64ERROR351
linux-devel-x86_64ERROR427
source / vignettesERROR299
linux-release-arm64ERROR324
linux-release-x86_64ERROR377
macos-release-arm64ERROR277
macos-release-x86_64ERROR436
macos-oldrel-arm64ERROR242
macos-oldrel-x86_64ERROR579
windows-develERROR339
windows-releaseERROR359
windows-oldrelERROR299
wasm-releaseOK179

Exports:.lemur_fitalign_by_groupingalign_harmonycompute_contrastsdesignfind_de_neighborhoodslemurproject_on_lemur_fitresidualstest_devars

Dependencies:abindassortheadbeachmatBiobaseBiocGenericsbiocmakeBiocNeighborsclicowplotcpp11DelayedArrayDelayedMatrixStatsdir.expirydplyrfarverfilelockgenericsGenomicRangesggplot2glmGamPoigluegtableh5mreadharmonyHDF5ArrayIRangesirlbaisobandlabelinglatticelifecyclelimmamagrittrMatrixMatrixGenericsmatrixStatspillarpkgconfigR6RColorBrewerRcppRcppArmadilloRcppProgressrhdf5rhdf5filtersRhdf5libRhpcBLASctlrlangS4ArraysS4VectorsS7scalesSeqinfoSingleCellExperimentSparseArraysparseMatrixStatsstatmodSummarizedExperimenttibbletidyselectutf8vctrsviridisLitewithrXVector