Provides functions for evaluating the stability of low-dimensional embeddings and cluster assignments in singleâcell RNA sequencing (scRNAâseq) datasets. Starting from a principal component analysis (PCA) object, users can generate multiple replicates of tâDistributed Stochastic Neighbor Embedding (tâSNE) or Uniform Manifold Approximation and Projection (UMAP) embeddings. Embedding stability is quantified by computing pairwise Kendallâs Tau correlations across replicates and summarizing the distribution of correlation coefficients. In addition to dimensionality reduction, 'scStability' assesses clustering consistency using either Louvain or Leiden algorithms and calculating the Normalized Mutual Information (NMI) between all pairs of cluster assignments. For background on UMAP and t-SNE algorithms, see McInnes et al. (2020, <doi:10.21105/joss.00861>) and van der Maaten & Hinton (2008, <https://github.com/lvdmaaten/bhtsne>), respectively.
Version: 1.0.3 Imports: aricode, future, future.apply, ggplot2, magrittr, pcaPP, rlang, Rtsne, Seurat, stats, uwot, vegan Suggests: spelling, knitr, rmarkdown, scRNAseq, SummarizedExperiment, BiocManager, testthat (≥ 3.0.0) Published: 2025-06-23 DOI: 10.32614/CRAN.package.scStability Author: Ben Abrahams [aut, cre] Maintainer: Ben Abrahams <ben.abrahams.de at gmail.com> License: MIT + file LICENSE NeedsCompilation: no Language: en-US Materials: README CRAN checks: scStability results Documentation: Downloads: Linking:Please use the canonical form https://CRAN.R-project.org/package=scStability to link to this page.
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