phenoTest

DOI: 10.18129/B9.bioc.phenoTest    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see phenoTest.

Tools to test association between gene expression and phenotype in a way that is efficient, structured, fast and scalable. We also provide tools to do GSEA (Gene set enrichment analysis) and copy number variation.

Bioconductor version: 3.8

Tools to test correlation between gene expression and phenotype in a way that is efficient, structured, fast and scalable. GSEA is also provided.

Author: Evarist Planet

Maintainer: Evarist Planet <evarist.planet at epfl.ch>

Installation

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

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

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("phenoTest")

 

PDF	R Script	Manual for the phenoTest library
PDF		Reference Manual

Details

biocViews	Classification, Clustering, DifferentialExpression, Microarray, MultipleComparison, Software
Version	1.30.0
In Bioconductor since	BioC 2.8 (R-2.13) (8 years)
License	GPL (>=2)
Depends	R (>= 2.12.0), Biobase, methods, annotate, Heatplus, BMA, ggplot2
Imports	survival, limma, Hmisc, gplots, Category, AnnotationDbi, hopach, biomaRt, GSEABase, genefilter, xtable, annotate, mgcv, SNPchip, hgu133a.db, HTSanalyzeR, ellipse
LinkingTo
Suggests	GSEABase, KEGG.db, GO.db
SystemRequirements
Enhances	parallel, org.Ce.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Hs.eg.db, org.Dm.eg.db
URL
Depends On Me
Imports Me	canceR
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	phenoTest_1.30.0.tar.gz
Windows Binary	phenoTest_1.30.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	phenoTest_1.30.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/phenoTest
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/phenoTest
Package Short Url	http://bioconductor.org/packages/phenoTest/
Package Downloads Report	Download Stats