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]

lemur_1.11.1.tar.gz
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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://huber-group-embl.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 11 exports 65 dependencies

Last updated from:376f2f9130. Checks:12 ERROR, 1 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-arm64ERROR335
linux-devel-x86_64ERROR348
source / vignettesERROR325
linux-release-arm64ERROR307
linux-release-x86_64ERROR378
macos-release-arm64ERROR275
macos-release-x86_64ERROR539
macos-oldrel-arm64ERROR269
macos-oldrel-x86_64ERROR510
windows-develERROR327
windows-releaseERROR313
windows-oldrelERROR357
wasm-releaseOK186

Exports:.lemur_fitalign_by_groupingalign_harmonycompute_contrastsdesignfind_de_neighborhoodslemurproject_on_lemur_fitresidualstest_devars

Dependencies:abindassortheadbeachmatBiobaseBiocGenericsbiocmakeBiocNeighborsclicowplotcpp11DelayedArrayDelayedMatrixStatsdir.expirydplyrfarverfilelockgenericsGenomicRangesggplot2glmGamPoigluegtableh5mreadharmonyHDF5ArrayIRangesirlbaisobandlabelinglatticelifecyclelimmamagrittrMatrixMatrixGenericsmatrixStatspillarpkgconfigR6RColorBrewerRcppRcppArmadilloRcppProgressrhdf5rhdf5filtersRhdf5libRhpcBLASctlrlangS4ArraysS4VectorsS7scalesSeqinfoSingleCellExperimentSparseArraysparseMatrixStatsstatmodSummarizedExperimenttibbletidyselectutf8vctrsviridisLitewithrXVector