Workflow Package: ExpressionNormalizationWorkflow

Gene Expression Normalization Workflow

Bioconductor version: Release (3.8)

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>

Citation (from within R, enter citation("ExpressionNormalizationWorkflow")):

Installation

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

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("ExpressionNormalizationWorkflow", version = "3.8")

Documentation

To view available workflows 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, Workflow
Version 1.6.0
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/
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