CellScore

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 (3.18)

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 googlemail.com>

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

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("CellScore")

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

Documentation

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

browseVignettes("CellScore")

R packages: CellScore	PDF	R Script
Reference Manual	PDF

Details

biocViews	DataImport, GeneExpression, Microarray, MultipleComparison, ReportWriting, Software, Transcription, Visualization
Version	1.21.4
In Bioconductor since	BioC 3.7 (R-3.5) (5.5 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
Linking To
Suggests	hgu133plus2CellScore, knitr, testthat (>= 3.0.0)
System Requirements
Enhances
URL

Depends On Me
Imports Me
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Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	CellScore_1.21.4.tar.gz
Windows Binary	CellScore_1.21.4.zip
macOS Binary (x86_64)	CellScore_1.21.4.tgz
macOS Binary (arm64)	CellScore_1.21.4.tgz
Source Repository	git clone https://git.bioconductor.org/packages/CellScore
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/CellScore
Bioc Package Browser	https://code.bioconductor.org/browse/CellScore/
Package Short Url	https://bioconductor.org/packages/CellScore/
Package Downloads Report	Download Stats