ExpressionNormalizationWorkflow

 

This is the development version of ExpressionNormalizationWorkflow; for the stable release version, see ExpressionNormalizationWorkflow.

Gene Expression Normalization Workflow

Bioconductor version: Development (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>

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

Installation

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

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("ExpressionNormalizationWorkflow", version = "3.9")

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 1.9.1
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_1.9.1.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 http://bioconductor.org/packages/ExpressionNormalizationWorkflow/
Package Downloads Report Download Stats

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