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 (3.20)
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 googlemail.com>
citation("CellScore")
):
Installation
To install this package, start R (version "4.4") 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 | R Script | |
Reference Manual |
Details
biocViews | DataImport, GeneExpression, Microarray, MultipleComparison, ReportWriting, Software, Transcription, Visualization |
Version | 1.25.0 |
In Bioconductor since | BioC 3.7 (R-3.5) (6.5 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 |
System Requirements | |
URL |
See More
Suggests | hgu133plus2CellScore, knitr, testthat (>= 3.0.0) |
Linking To | |
Enhances | |
Depends On Me | |
Imports Me | |
Suggests Me | homosapienDEE2CellScore |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | CellScore_1.25.0.tar.gz |
Windows Binary | CellScore_1.25.0.zip (64-bit only) |
macOS Binary (x86_64) | CellScore_1.25.0.tgz |
macOS Binary (arm64) | CellScore_1.25.0.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 |