Package: slalom 1.29.0
Davis McCarthy
slalom: Factorial Latent Variable Modeling of Single-Cell RNA-Seq Data
slalom is a scalable modelling framework for single-cell RNA-seq data that uses gene set annotations to dissect single-cell transcriptome heterogeneity, thereby allowing to identify biological drivers of cell-to-cell variability and model confounding factors. The method uses Bayesian factor analysis with a latent variable model to identify active pathways (selected by the user, e.g. KEGG pathways) that explain variation in a single-cell RNA-seq dataset. This an R/C++ implementation of the f-scLVM Python package. See the publication describing the method at https://doi.org/10.1186/s13059-017-1334-8.
Authors:
slalom_1.29.0.tar.gz
slalom_1.29.0.zip(r-4.5)slalom_1.29.0.zip(r-4.4)slalom_1.29.0.zip(r-4.3)
slalom_1.29.0.tar.gz(r-4.5-noble)slalom_1.29.0.tar.gz(r-4.4-noble)
slalom.pdf |slalom.html✨
slalom/json (API)
NEWS
| # Install 'slalom' in R: |
| install.packages('slalom', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- mesc - A single-cell expression dataset to demonstrate capabilities of slalom from mouse embryonic stem cells
On BioConductor:slalom-1.29.0(bioc 3.21)slalom-1.28.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
immunooncologysinglecellrnaseqnormalizationvisualizationdimensionreductiontranscriptomicsgeneexpressionsequencingsoftwarereactomekegg
Last updated 20 days agofrom:9d5e3d4cc7. Checks:OK: 1 WARNING: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 31 2024 |
| R-4.5-win-x86_64 | WARNING | Oct 31 2024 |
| R-4.5-linux-x86_64 | WARNING | Oct 31 2024 |
| R-4.4-win-x86_64 | WARNING | Oct 31 2024 |
| R-4.3-win-x86_64 | WARNING | Oct 31 2024 |
Exports:addResultsToSingleCellExperimentinitSlalomnewSlalomModelplotLoadingsplotRelevanceplotTermstopTermstrainSlalomupdateSlalom
Dependencies:abindannotateAnnotationDbiaskpassBHBiobaseBiocGenericsBiostringsbitbit64blobcachemclicolorspacecpp11crayoncurlDBIDelayedArrayfansifarverfastmapGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegraphGSEABasegtablehttrIRangesisobandjsonliteKEGGRESTlabelinglatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrpngR6RColorBrewerRcppRcppArmadillorlangRSQLitersvdS4ArraysS4VectorsscalesSingleCellExperimentSparseArraySummarizedExperimentsystibbleUCSC.utilsutf8vctrsviridisLitewithrXMLxtableXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Add results to SingleCellExperiment object | addResultsToSingleCellExperiment |
| Initialize a SlalomModel object | initSlalom |
| A single-cell expression dataset to demonstrate capabilities of slalom from mouse embryonic stem cells (mESCs) | mesc |
| Create a new SlalomModel object. | newSlalomModel |
| Plot highest loadings of a factor | plotLoadings |
| Plot results of a Slalom model | plotRelevance |
| Plot relevance for all terms | plotTerms |
| The "Slalom Model" (Rcpp_SlalomModel) class | Rcpp_SlalomModel Rcpp_SlalomModel-class |
| Factorial single-cell latent variable models | slalom-package slalom |
| SlalomModel C++ class | SlalomModel |
| Show results of a Slalom model | topTerms |
| Train a SlalomModel object | train train,Rcpp_SlalomModel-method trainSlalom |
| Update a SlalomModel object | updateSlalom |
