To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("ALDEx2")

In most cases, you don't need to download the package archive at all.

ALDEx2

 

   

Analysis Of Differential Abundance Taking Sample Variation Into Account

Bioconductor version: Release (3.5)

A differential abundance analysis for the comparison of two or more conditions. For example, single-organism and meta-RNA-seq high-throughput sequencing assays, or of selected and unselected values from in-vitro sequence selections. Uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected false discovery rate given the biological and sampling variation using the Wilcox rank test or Welches t-test (aldex.ttest) or the glm and Kruskal Wallis tests (aldex.glm). Reports both P and fdr values calculated by the Benjamini Hochberg correction.

Author: Greg Gloor, Ruth Grace Wong, Andrew Fernandes, Arianne Albert, Matt Links, Jia Rong Wu

Maintainer: Greg Gloor <ggloor at uwo.ca>

Citation (from within R, enter citation("ALDEx2")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("ALDEx2")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ALDEx2")

 

PDF R Script An R Package for determining differential abundance in high throughput sequencing experiments
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews Bayesian, ChIPSeq, DNASeq, DifferentialExpression, GeneExpression, Metagenomics, Microbiome, RNASeq, Sequencing, Software
Version 1.8.0
In Bioconductor since BioC 3.0 (R-3.1) (2.5 years)
License file LICENSE
Depends methods
Imports S4Vectors, IRanges, GenomicRanges, SummarizedExperiment, BiocParallel
LinkingTo
Suggests
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source ALDEx2_1.8.0.tar.gz
Windows Binary ALDEx2_1.8.0.zip
Mac OS X 10.11 (El Capitan) ALDEx2_1.8.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/ALDEx2/tree/release-3.5
Package Short Url http://bioconductor.org/packages/ALDEx2/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: