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This is the development version of CellScore; for the stable release version, see CellScore.

Tool for Evaluation of Cell Identity from Transcription Profiles

Bioconductor version: Development (3.20)

The CellScore package contains functions to evaluate the cell identity of a test sample, given a cell transition defined with a starting (donor) cell type and a desired target cell type. The evaluation is based upon a scoring system, which uses a set of standard samples of known cell types, as the reference set. The functions have been carried out on a large set of microarray data from one platform (Affymetrix Human Genome U133 Plus 2.0). In principle, the method could be applied to any expression dataset, provided that there are a sufficient number of standard samples and that the data are normalized.

Author: Nancy Mah [aut, cre], Katerina Taskova [aut], Justin Marsh [aut]

Maintainer: Nancy Mah <nancy.l.mah at>

Citation (from within R, enter citation("CellScore")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

R packages: CellScore PDF R Script
Reference Manual PDF


biocViews DataImport, GeneExpression, Microarray, MultipleComparison, ReportWriting, Software, Transcription, Visualization
Version 1.25.0
In Bioconductor since BioC 3.7 (R-3.5) (6 years)
License GPL-3
Depends R (>= 4.3.0)
Imports Biobase(>= 2.39.1), graphics (>= 3.5.0), grDevices (>= 3.5.0), gplots (>= 3.0.1), lsa (>= 0.73.1), methods (>= 3.5.0), RColorBrewer (>= 1.1-2), squash (>= 1.0.8), stats (>= 3.5.0), utils (>= 3.5.0), SummarizedExperiment
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Suggests hgu133plus2CellScore, knitr, testthat (>= 3.0.0)
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Source Package CellScore_1.25.0.tar.gz
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macOS Binary (x86_64) CellScore_1.25.0.tgz
macOS Binary (arm64) CellScore_1.25.0.tgz
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