CellScore
Tool for Evaluation of Cell Identity from Transcription Profiles
Bioconductor version: Release (3.19)
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")
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 | 1.24.0 |
| 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_1.24.0.tar.gz |
| Windows Binary (x86_64) | CellScore_1.24.0.zip |
| macOS Binary (x86_64) | CellScore_1.24.0.tgz |
| macOS Binary (arm64) | CellScore_1.24.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/CellScore |
| Source Repository (Developer Access) | git clone [email protected]:packages/CellScore |
| Bioc Package Browser | https://code.bioconductor.org/browse/CellScore/ |
| Package Short Url | https://bioconductor.org/packages/CellScore/ |
| Package Downloads Report | Download Stats |