Package: scCertify 0.99.1

Jaya Surya Doddetipalli

scCertify: Explainable Confidence Scoring for Single-Cell Annotations

cellCertR provides an explainable confidence scoring framework for single-cell RNA sequencing annotations using marker enrichment, neighborhood agreement, entropy-based uncertainty estimation, and ontology-aware label matching.

Authors:Jaya Surya Doddetipalli [aut, cre]

scCertify_0.99.1.tar.gz
scCertify_0.99.1.zip(r-4.7)scCertify_0.99.1.zip(r-4.6)scCertify_0.99.1.zip(r-4.5)
scCertify_0.99.1.tgz(r-4.6-any)scCertify_0.99.1.tgz(r-4.5-any)
scCertify_0.99.1.tar.gz(r-4.7-any)scCertify_0.99.1.tar.gz(r-4.6-any)
scCertify_0.99.1.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://biocstaging.r-universe.dev', 'https://cloud.r-project.org'))

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

On CRAN:

software singlecell rnaseq geneexpression sequencing

3.00 score 9 exports 166 dependencies

Last updated from:0a6e8bebd2. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	248
linux-devel-x86_64	OK	218
source / vignettes	OK	356
linux-release-x86_64	OK	239
macos-release-arm64	OK	148
macos-oldrel-arm64	OK	149
windows-devel	OK	977
windows-release	OK	993
windows-oldrel	OK	1001
wasm-release	OK	253

Exports:calibrate_confidence cell_certify classify_confidence entropy_score explain_cell explain_confidence marker_score match_labels 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 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 Workflow

Rendered fromscCertify-workflow.Rmdusingknitr::rmarkdown

Last update: 2026-07-01
Started: 2026-05-15

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Calibrate Confidence Scores	calibrate_confidence
Cell Annotation Confidence	cell_certify
Classify Confidence Levels	classify_confidence
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
Neighbor Agreement Score	neighbor_score