hgu133plus2CellScore

DOI: 10.18129/B9.bioc.hgu133plus2CellScore    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see hgu133plus2CellScore.

CellScore Standard Cell Types Expression Dataset [hgu133plus2]

Bioconductor version: 3.8

The CellScore Standard Dataset contains expression data from a wide variety of human cells and tissues, which should be used as standard cell types in the calculation of the CellScore. All data was curated from public databases such as Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov/geo/) or ArrayExpress (https://www.ebi.ac.uk/arrayexpress/). This standard dataset only contains data from the Affymetrix GeneChip Human Genome U133 Plus 2.0 microarrays. Samples were manually annotated using the database information or consulting the publications in which the datasets originated. The sample annotations are stored in the phenoData slot of the expressionSet object. Raw data (CEL files) were processed with the affy package to generate present/absent calls (mas5calls) and background-subtracted values, which were then normalized by the R-package yugene to yield the final expression values for the standard expression matrix. The annotation table for the microarray was retrieved from the BioC annotation package hgu133plus2. All data are stored in an expressionSet object.

Author: Nancy Mah, Katerina Taskova

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

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("hgu133plus2CellScore")

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("hgu133plus2CellScore")

 

PDF	R Script	R packages: hgu133plus2CellScore
PDF		Reference Manual

Details

biocViews	ArrayExpress, ExperimentData, ExpressionData, GEO, Genome, Homo_sapiens_Data, MicroarrayData
Version	1.2.0
License	GPL-3
Depends	R (>= 3.5.0)
Imports	Biobase(>= 2.39.1)
LinkingTo
Suggests	knitr
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me	CellScore
Links To Me
Build Report

Package Archives

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

Source Package	hgu133plus2CellScore_1.2.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)
Source Repository	git clone https://git.bioconductor.org/packages/hgu133plus2CellScore
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/hgu133plus2CellScore
Package Short Url	http://bioconductor.org/packages/hgu133plus2CellScore/
Package Downloads Report	Download Stats