ExpressionNormalizationWorkflow

DOI: 10.18129/B9.bioc.ExpressionNormalizationWorkflow    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see ExpressionNormalizationWorkflow.

Gene Expression Normalization Workflow

Bioconductor version: 3.9

An extensive, customized expression normalization workflow incorporating Supervised Normalization of Microarryas(SNM), Surrogate Variable Analysis(SVA) and Principal Variance Component Analysis to identify batch effects and remove them from the expression data to enhance the ability to detect the underlying biological signals.

Author: Karthikeyan Murugesan [aut, cre], Greg Gibson [sad, ths]

Maintainer: Karthikeyan Murugesan <karthikeyanm60 at yahoo.com>

Installation

To install this package, start R (version "3.6") and enter:

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

BiocManager::install("ExpressionNormalizationWorkflow")

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("ExpressionNormalizationWorkflow")

 

HTML

R Script

Gene Expression Normalization Workflow

Details

biocViews	GeneExpressionWorkflow, ImmunoOncologyWorkflow, Workflow
Version	1.10.0
License	GPL (>=3)
Depends
Imports	Biobase(>= 2.24.0), limma(>= 3.20.9), lme4 (>= 1.1.7), matrixStats (>= 0.10.3), pvca(>= 1.4.0), snm(>= 1.12.0), sva(>= 3.10.0), vsn(>= 3.32.0)
LinkingTo
Suggests	knitr, BiocStyle
SystemRequirements
Enhances
URL
BugReports	https://github.com/
Depends On Me
Imports Me
Suggests Me
Links To Me

Package Archives

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

Source Package	ExpressionNormalizationWorkflow_1.10.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)
Source Repository	git clone https://git.bioconductor.org/packages/ExpressionNormalizationWorkflow
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ExpressionNormalizationWorkflow
Package Short Url	https://bioconductor.org/packages/ExpressionNormalizationWorkflow/
Package Downloads Report	Download Stats