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✨
DESCRIPTION |NEWS
card.svg |card.png
lemur/json (API)

# 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-1.11.1(bioc 3.24)lemur-1.9.0(bioc 3.23)

transcriptomicsdifferentialexpressionsinglecelldimensionreductionregressionquartoopenblascpp

6.98 score 102 stars 117 scripts 11 exports 65 dependencies

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

TargetResultTimeFilesSyslog
bioc-checksWARNING209
linux-devel-arm64ERROR339
linux-devel-x86_64ERROR353
source / vignettesERROR320
linux-release-arm64ERROR311
linux-release-x86_64ERROR355
macos-release-arm64ERROR239
macos-release-x86_64ERROR595
macos-oldrel-arm64ERROR214
macos-oldrel-x86_64ERROR485
windows-develERROR577
windows-releaseERROR348
windows-oldrelERROR482
wasm-releaseOK178

Exports:.lemur_fitalign_by_groupingalign_harmonycompute_contrastsdesignfind_de_neighborhoodslemurproject_on_lemur_fitresidualstest_devars

Dependencies:abindassortheadbeachmatBiobaseBiocGenericsbiocmakeBiocNeighborsclicowplotcpp11DelayedArrayDelayedMatrixStatsdir.expirydplyrfarverfilelockgenericsGenomicRangesggplot2glmGamPoigluegtableh5mreadharmonyHDF5ArrayIRangesirlbaisobandlabelinglatticelifecyclelimmamagrittrMatrixMatrixGenericsmatrixStatspillarpkgconfigR6RColorBrewerRcppRcppArmadilloRcppProgressrhdf5rhdf5filtersRhdf5libRhpcBLASctlrlangS4ArraysS4VectorsS7scalesSeqinfoSingleCellExperimentSparseArraysparseMatrixStatsstatmodSummarizedExperimenttibbletidyselectutf8vctrsviridisLitewithrXVector