scTypeEval
This is the development version of scTypeEval; to use it, please install the devel version of Bioconductor.
Evaluation of cell type classifications in single-cell transcriptomics
Bioconductor version: Development (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")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("scTypeEval")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | CellBasedAssays, DimensionReduction, GeneExpression, Preprocessing, PrincipalComponent, SingleCell, Software, Transcriptomics |
| Version | 0.99.30 |
| In Bioconductor since | BioC 3.23 (R-4.6) |
| License | GPL-3 + file LICENSE |
| Depends | R (>= 4.6.0) |
| 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 |
| Linking To | |
| Enhances | |
| Depends On Me | |
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| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (big-sur-arm64) | |
| macOS Binary (sonoma-arm64) | |
| 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 |