CellMentor
Supervised Non-negative Matrix Factorization for Dimensional Reduction in Single-Cell Analysis
Bioconductor version: 3.24 · Package version: 1.1.2
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
Implements supervised cell type-aware non-negative matrix factorization (NMF) for dimensional reduction in single-cell RNA sequencing analysis. The package provides methods for incorporating cell type information into the dimensionality reduction process, enabling improved visualization and downstream analysis of single-cell data while preserving biological structure. CellMentor employs a unique loss function that simultaneously minimizes variation within known cell populations while maximizing distinctions between different cell types, enabling effective transfer of learned patterns from labeled reference datasets to new unlabeled data.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("CellMentor")Details
| Maintainer | Ekaterina Petrenko <petrenko.kate@icloud.com> |
| Author | Ekaterina Petrenko [aut, cre] (ORCID: <https://orcid.org/0000-0003-3549-834X>) |
| License | Apache License (>= 2) |
| URL | https://github.com/petrenkokate/CellMentor |
| Bug Reports | https://github.com/petrenkokate/CellMentor/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | DimensionReduction, SingleCell, Software, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/CellMentor/ |
Citation
From within R, enter citation("CellMentor"):
Ekaterina Petrenko. CellMentor: Supervised Non-negative Matrix Factorization for Dimensional Reduction in Single-Cell Analysis. doi:10.18129/B9.bioc.CellMentor, R package version 1.1.2, https://bioconductor.org/packages/CellMentor.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | CellMentor_1.1.2.tar.gz |
| Windows binary (x86_64) | CellMentor_1.1.2.zip |
| macOS binary (arm64) | CellMentor_1.1.2.tgz |
| macOS binary (x86_64) | CellMentor_1.1.2.tgz |
Dependencies
Depends: R (>= 4.5.0)
Imports: methods, Matrix, BiocParallel, SingleR, Seurat (>= 4.0.0), utils, stats, parallel, progress, ggplot2, data.table, magrittr, graphics, RMTstat, sparsesvd, cluster, skmeans, MLmetrics, tibble, lsa, nnls, SingleCellExperiment, entropy, irlba, aricode
Suggests: testthat (>= 3.0.0), covr, withr, rmarkdown, knitr, BiocStyle, scater, scRNAseq