scTypeEval
This is the released version of scTypeEval; for the devel version, see scTypeEval.
Evaluation of cell type classifications in single-cell transcriptomics
Bioconductor version: Release (3.23)
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.
Author: Josep Garnica [aut, cre] 
, Massimo Andreatta [aut] , Santiago Carmona [aut]
Maintainer: Josep Garnica <josep.garnicacaparros at unige.ch>
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 1.0.0, https://bioconductor.org/packages/scTypeEval.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("scTypeEval")For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("scTypeEval")| Quick Start Guide | HTML | R Script |
| scTypeEval: Evaluating Cell Type Classifications | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | CellBasedAssays, DimensionReduction, GeneExpression, Preprocessing, PrincipalComponent, SingleCell, Software, Transcriptomics |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.23 (R-4.6) (< 6 months) |
| License | GPL-3 + file LICENSE |
| 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 |
| System Requirements | |
| URL | https://github.com/carmonalab/scTypeEval |
| Bug Reports | https://github.com/carmonalab/scTypeEval/issues |
See More
| 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 |
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| Depends On Me | |
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| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | scTypeEval_1.0.0.tar.gz |
| Windows Binary (x86_64) | scTypeEval_1.0.0.zip |
| macOS Binary (big-sur-x86_64) | scTypeEval_1.0.0.tgz |
| macOS Binary (sonoma-arm64) | scTypeEval_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/scTypeEval |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/scTypeEval |
| Package Short Url | https://bioconductor.org/packages/scTypeEval/ |
| Package Downloads Report | Download Stats |