scCertify
This is the development version of scCertify; to use it, please install the devel version of Bioconductor.
Explainable Confidence Scoring for Single-Cell Annotations
Bioconductor version: 3.24 · Package version: 0.99.7
scCertify provides an explainable framework for assessing the confidence of cell-type annotations in single-cell RNA sequencing data. Confidence scores are computed using marker enrichment, neighborhood agreement, entropy-based uncertainty estimation, and ontology-aware label matching to support transparent interpretation of annotation quality.
Author: Jaya Surya Doddetipalli [aut, cre] 
Maintainer: Jaya Surya Doddetipalli <jayasuryadoddetipalli at gmail.com>
Citation
From within R, enter citation("scCertify"):
Jaya Surya Doddetipalli. scCertify: Explainable Confidence Scoring for Single-Cell Annotations. doi:10.18129/B9.bioc.scCertify, R package version 0.99.7, https://bioconductor.org/packages/scCertify.
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("scCertify")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 0.99.7 |
| License | MIT + file LICENSE |
| URL | https://github.com/Jaya-Surya-dev/scCertify |
| Bug Reports | https://github.com/Jaya-Surya-dev/scCertify/issues |
| Last updated | 2026-08-21 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| Downloads rank | 2439 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | GeneExpression, RNASeq, Sequencing, SingleCell, Software |
| Package Short Url | https://bioconductor.org/packages/scCertify/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("scCertify")| scCertify: Explainable Confidence Scoring for Single-Cell Annotations | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | scCertify_0.99.7.tar.gz |
| Windows binary (x86_64) | scCertify_0.99.7.zip |
| macOS binary (arm64) | scCertify_0.99.7.tgz |
| macOS binary (x86_64) | scCertify_0.99.7.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/scCertify |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/scCertify |
| Package Downloads Report | Download Stats |
Dependencies
Imports: Seurat, SingleCellExperiment, SummarizedExperiment, FNN, entropy, UCell
Suggests: BiocStyle, SingleR, celldex, ggplot2, knitr, rmarkdown, scDblFinder, SeuratObject, testthat (>= 3.0.0)