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ExpressionNormalizationWorkflow

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

Gene Expression Normalization Workflow


Bioconductor version: Development (3.21)

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 "4.5") and enter: 


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
Gene Expression Normalization Workflow HTML R Script

Need some help? Ask on the Bioconductor Support site!

Details

biocViews GeneExpressionWorkflow, ImmunoOncologyWorkflow, Workflow
Version 1.32.0
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)
System Requirements
URL
Bug Reports https://github.com/
See More
Suggests knitr, BiocStyle
Linking To
Enhances
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Package Archives

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

Source Package ExpressionNormalizationWorkflow_1.32.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/ExpressionNormalizationWorkflow
Source Repository (Developer Access) git clone [email protected]:packages/ExpressionNormalizationWorkflow
Package Short Url https://bioconductor.org/packages/ExpressionNormalizationWorkflow/
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