CellScore

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see CellScore.

Tool for Evaluation of Cell Identity from Transcription Profiles


Bioconductor version: 3.17

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, Katerina Taskova

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")

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 1.20.0
In Bioconductor since BioC 3.7 (R-3.5) (6 years)
License GPL-3
Depends R (>= 3.5.0)
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)
System Requirements
URL
See More
Suggests hgu133plus2CellScore, knitr
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package CellScore_1.20.0.tar.gz
Windows Binary CellScore_1.20.0.zip
macOS Binary (x86_64) CellScore_1.20.0.tgz
macOS Binary (arm64) CellScore_1.20.0.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
Old Source Packages for BioC 3.17 Source Archive