Package: scCertify 0.99.9

Jaya Surya Doddetipalli

scCertify: Explainable Confidence Scoring for Single-Cell Annotations

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.

Authors:Jaya Surya Doddetipalli [aut, cre]

scCertify_0.99.9.tar.gz
scCertify_0.99.9.zip(r-4.7-any)scCertify_0.99.9.zip(r-4.6-any)scCertify_0.99.9.zip(r-4.5-any)
scCertify_0.99.9.tgz(r-4.6-any)scCertify_0.99.9.tgz(r-4.5-any)
scCertify_0.99.9.tar.gz(r-4.7-any)scCertify_0.99.9.tar.gz(r-4.6-any)
scCertify_0.99.9.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
scCertify/json (API)

# Install 'scCertify' in R:

install.packages('scCertify', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/jaya-surya-dev/sccertify/issues

On BioConductor:scCertify-0.99.8(bioc 3.24)

software singlecell rnaseq geneexpression sequencing bioinformatics scrna-seq seurat single-cell single-cell-rna-seq uncertainity-estimation

4.54 score 1 stars 166 downloads 13 exports 167 dependencies

Last updated from:6f9948caf4. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	336
linux-devel	OK	322
source / vignettes	OK	530
linux-release	OK	521
macos-release	OK	154
macos-oldrel	OK	173
windows-devel	OK	2033
windows-release	OK	2238
windows-oldrel	OK	2015
wasm-release	OK	263

Exports:calibrate_confidence cell_certify classify_confidence de_novo_signatures discovery_aware discovery_status entropy_score explain_cell explain_confidence marker_score match_labels negative_marker_score neighbor_score

Dependencies:abind askpass assorthead base64enc beachmat BH Biobase BiocGenerics BiocNeighbors BiocParallel bitops bslib cachem caTools cli cluster codetools commonmark cowplot cpp11 crosstalk curl data.table DelayedArray deldir digest dotCall64 dplyr dqrng entropy evaluate farver fastDummies fastmap fitdistrplus FNN fontawesome formatR fs futile.logger futile.options future future.apply generics GenomicRanges ggplot2 ggrepel ggridges globals glue goftest gplots gridExtra gtable gtools here highr htmltools htmlwidgets httpuv httr ica igraph IRanges irlba isoband jquerylib jsonlite KernSmooth knitr labeling lambda.r later lattice lazyeval lifecycle listenv lmtest magrittr MASS Matrix MatrixGenerics matrixStats memoise mime miniUI nlme openssl otel parallelly patchwork pbapply pillar pkgconfig plotly plyr png polyclip progressr promises purrr R6 RANN rappdirs RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppHNSW RcppProgress RcppThread RcppTOML reshape2 reticulate rlang rmarkdown ROCR rprojroot RSpectra Rtsne S4Arrays S4Vectors S7 sass scales scattermore sctransform Seqinfo Seurat SeuratObject shiny SingleCellExperiment sitmo snow sourcetools sp spam SparseArray spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.univar spatstat.utils stringi stringr SummarizedExperiment survival sys tensor tibble tidyr tidyselect tinytex UCell utf8 uwot vctrs viridisLite withr xfun xtable XVector yaml zoo

scCertify: Explainable Confidence Scoring for Single-Cell Annotations

Rendered fromscCertify-workflow.Rmdusingknitr::rmarkdown

Last update: 2026-08-21
Started: 2026-05-15

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Help page	Topics
scCertify: Explainable Confidence Scoring for Single-Cell Annotations	scCertify-package scCertify
Calibrate Confidence Scores	calibrate_confidence
Cell Annotation Confidence	cell_certify
Classify Confidence Levels	classify_confidence
Cluster-Enriched Gene Signatures	de_novo_signatures
Discovery-Aware Annotation Analysis	discovery_aware
Discovery-Aware Annotation Status	discovery_status
Entropy-Based Uncertainty Score	entropy_score
Explain Cell Annotation Confidence	explain_cell
Explain Confidence Attribution	explain_confidence
Marker Consistency Score	marker_score
Ontology Label Matching	match_labels
Negative Marker Consistency Score	negative_marker_score
Neighbor Agreement Score	neighbor_score

Package: scCertify 0.99.9

scCertify: Explainable Confidence Scoring for Single-Cell Annotations

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)