scTypeEval
Evaluation of cell type classifications in single-cell transcriptomics
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)
scTypeEval provides tools to evaluate and validate cell type classifications in single-cell transcriptomics when ground truth labels are limited or unavailable. Results are organized in an S4 object that integrates processed data, dimensional reductions, dissimilarity assays, and consistency metrics computed across samples. The workflow includes preprocessing and feature selection, principal component analysis, computation of dissimilarity matrices, internal validation metrics (for example, silhouette-based summaries), and visualization utilities to inspect heatmaps and PCA plots. Functions support common single-cell containers and enable comparison of clustering and labeling strategies across datasets.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("scTypeEval")Details
| Maintainer | Josep Garnica <josep.garnicacaparros@unige.ch> |
| Author | Josep Garnica [aut, cre] (ORCID: <https://orcid.org/0000-0001-9493-1321>), Massimo Andreatta [aut] (ORCID: <https://orcid.org/0000-0002-8036-2647>), Santiago Carmona [aut] (ORCID: <https://orcid.org/0000-0002-2495-0671>) |
| License | GPL-3 + file LICENSE |
| URL | https://github.com/carmonalab/scTypeEval |
| Bug Reports | https://github.com/carmonalab/scTypeEval/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | CellBasedAssays, DimensionReduction, GeneExpression, Preprocessing, PrincipalComponent, SingleCell, Software, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/scTypeEval/ |
Citation
From within R, enter citation("scTypeEval"):
Josep Garnica, Massimo Andreatta, Santiago Carmona. scTypeEval: Evaluation of cell type classifications in single-cell transcriptomics. doi:10.18129/B9.bioc.scTypeEval, R package version 1.1.2, https://bioconductor.org/packages/scTypeEval.
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 | scTypeEval_1.1.2.tar.gz |
| Windows binary (x86_64) | scTypeEval_1.1.2.zip |
| macOS binary (arm64) | scTypeEval_1.1.2.tgz |
| macOS binary (x86_64) | scTypeEval_1.1.2.tgz |
Dependencies
Depends: R (>= 4.5.0)
Imports: Matrix (>= 1.6-5), BiocParallel (>= 1.34.2), dplyr (>= 1.1.4), tidyr (>= 1.3.1), scran (>= 1.30.2), bluster (>= 1.12.0), ggplot2 (>= 3.5.1), ggrepel (>= 0.9.6), cluster (>= 2.1.4), SingleR (>= 2.4.1), irlba (>= 2.3.5.1), transport (>= 0.15-4), grDevices, methods, stats, utils
Suggests: testthat (>= 3.0.0), transformGamPoi (>= 1.8.0), glmGamPoi (>= 1.14.3), anndata (>= 0.8.0), SummarizedExperiment (>= 1.32.0), igraph (>= 2.1.1), Seurat, SingleCellExperiment, knitr, rmarkdown, BiocStyle, BiocManager, SeuratObject, ggpubr, rlang, stringr, tibble