Package: lemur 1.10.0
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:
lemur_1.10.0.tar.gz
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lemur_1.10.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
lemur/json (API)
NEWS
| # Install 'lemur' in R: |
| install.packages('lemur', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/const-ae/lemur/issues
- glioblastoma_example_data - The 'glioblastoma_example_data' dataset
On BioConductor:lemur-1.11.1(bioc 3.24)lemur-1.9.0(bioc 3.23)
transcriptomicsdifferentialexpressionsinglecelldimensionreductionregressionquartoopenblascpp
Last updated from:ed31ad1874 (on RELEASE_3_23). Checks:1 WARNING, 12 ERROR, 1 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 207 | ||
| linux-devel-arm64 | ERROR | 313 | ||
| linux-devel-x86_64 | ERROR | 435 | ||
| source / vignettes | ERROR | 302 | ||
| linux-release-arm64 | ERROR | 353 | ||
| linux-release-x86_64 | ERROR | 361 | ||
| macos-release-arm64 | ERROR | 308 | ||
| macos-release-x86_64 | ERROR | 367 | ||
| macos-oldrel-arm64 | ERROR | 268 | ||
| macos-oldrel-x86_64 | ERROR | 399 | ||
| windows-devel | ERROR | 382 | ||
| windows-release | ERROR | 326 | ||
| windows-oldrel | ERROR | 346 | ||
| wasm-release | OK | 171 |
Exports:.lemur_fitalign_by_groupingalign_harmonydesignfind_de_neighborhoodslemurproject_on_lemur_fitresidualstest_devars
Dependencies:abindassortheadbeachmatBiobaseBiocGenericsbiocmakeBiocNeighborsclicowplotcpp11DelayedArrayDelayedMatrixStatsdir.expirydplyrfarverfilelockgenericsGenomicRangesggplot2glmGamPoigluegtableh5mreadharmonyHDF5ArrayIRangesirlbaisobandlabelinglatticelifecyclelimmamagrittrMatrixMatrixGenericsmatrixStatspillarpkgconfigR6RColorBrewerRcppRcppArmadilloRcppProgressrhdf5rhdf5filtersRhdf5libRhpcBLASctlrlangS4ArraysS4VectorsS7scalesSeqinfoSingleCellExperimentSparseArraysparseMatrixStatsstatmodSummarizedExperimenttibbletidyselectutf8vctrsviridisLitewithrXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Access values from a 'lemur_fit' | $,lemur_fit-method $<-,lemur_fit-method .DollarNames.lemur_fit dollar_methods |
| Enforce additional alignment of cell clusters beyond the direct differential embedding | align_by_grouping align_harmony |
| Find differential expression neighborhoods | find_de_neighborhoods |
| The 'glioblastoma_example_data' dataset | glioblastoma_example_data |
| Main function to fit the latent embedding multivariate regression (LEMUR) model | lemur |
| The 'lemur_fit' class | .lemur_fit design,lemur_fit-method lemur_fit lemur_fit-class [,lemur_fit,ANY,ANY,ANY-method |
| Predict values from 'lemur_fit' object | predict.lemur_fit |
| Project new data onto the latent spaces of an existing lemur fit | project_on_lemur_fit |
| Predict values from 'lemur_fit' object | residuals,lemur_fit-method |
| Predict log fold changes between conditions for each cell | test_de |
| Differential embedding for each condition | test_global |
