Package 'scCertify'

Title: Explainable Confidence Scoring for Single-Cell Annotations
Description: 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] (ORCID: <https://orcid.org/0009-0002-8975-4425>)
Maintainer: Jaya Surya Doddetipalli <[email protected]>
License: MIT + file LICENSE
Version: 0.99.1
Built: 2026-07-01 15:46:08 UTC
Source: https://github.com/BiocStaging/scCertify

Help Index

Calibrate Confidence Scores

Description

Converts raw confidence scores into calibrated percentile scores.

Usage

calibrate_confidence(scores)

Arguments

scores

Numeric vector

Value

Numeric vector

Examples

scores <- c(
  0.2,
  0.5,
  0.8
)

calibrate_confidence(
  scores
)

Cell Annotation Confidence

Description

Main confidence scoring framework.

Usage

cell_certify(object, markers, label_column = "predicted_label")

Arguments

object

Seurat object
markers

Named marker list
label_column

Metadata label column

Value

Seurat object

Examples

NULL

Classify Confidence Levels

Description

Converts confidence scores into confidence classes.

Usage

classify_confidence(scores)

Arguments

scores

Numeric vector

Value

Character vector

Examples

scores <- c(
  0.2,
  0.7,
  0.9
)

classify_confidence(
  scores
)

Entropy-Based Uncertainty Score

Description

Calculates entropy from prediction score matrices.

Usage

entropy_score(score_matrix)

Arguments

score_matrix

Numeric matrix

Value

Numeric vector

Examples

mat <- matrix(
  runif(20),
  nrow = 5
)

entropy_score(
  mat
)

Explain Cell Annotation Confidence

Description

Provides interpretable explanation for confidence scores.

Usage

explain_cell(object, cell_id)

Arguments

object

Seurat object
cell_id

Cell barcode

Value

Character vector

Examples

NULL

Explain Confidence Attribution

Description

Explains why a cell received its confidence score.

Usage

explain_confidence(object, cell_id)

Arguments

object

Seurat object
cell_id

Cell barcode

Value

Character vector

Examples

NULL

Marker Consistency Score

Description

Uses UCell enrichment scoring for marker evaluation.

Usage

marker_score(object, markers, label_column = "predicted_label")

Arguments

object

Seurat object
markers

Named marker list
label_column

Metadata label column

Value

Numeric vector

Examples

NULL

Ontology Label Matching

Description

Matches predicted labels to marker database labels.

Usage

match_labels(label, marker_names)

Arguments

label

Character label
marker_names

Character vector

Value

Character vector

Examples

match_labels(
  "T_cells",
  c(
    "T_cell",
    "B_cell"
  )
)

Neighbor Agreement Score

Description

Computes local neighborhood agreement scores.

Usage

neighbor_score(
  object,
  reduction = "pca",
  dims = NULL,
  k = 10,
  label_column = "predicted_label"
)

Arguments

object

Seurat object
reduction

Reduction method
dims

PCA dimensions
k

Number of neighbors
label_column

Metadata label column

Value

Numeric vector

Examples

NULL