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>
citation("ExpressionNormalizationWorkflow")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("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")| Gene Expression Normalization Workflow | HTML | R Script |
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) |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/ |
See More
| Suggests | knitr, BiocStyle |
| Linking To | |
| Enhances | |
| 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 [email protected]:packages/ExpressionNormalizationWorkflow |
| Package Short Url | https://bioconductor.org/packages/ExpressionNormalizationWorkflow/ |
| Package Downloads Report | Download Stats |