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

 

   

This is the development version of ALDEx2; for the stable release version, see ALDEx2.

Analysis Of Differential Abundance Taking Sample Variation Into Account

Bioconductor version: Development (3.6)

A differential abundance analysis for the comparison of two or more conditions. Useful for analyzing data from standard RNA-seq or meta-RNA-seq assays as well as selected and unselected values from in-vitro sequence selections. Uses a Dirichlet-multinomial model to infer abundance from counts, optimized for three or more experimental replicates. The method infers biological and sampling variation to calculate the expected false discovery rate, given the variation, based on a Wilcox rank test or Welch t-test (via aldex.ttest), or a glm and Kruskal-Wallis test (via aldex.glm). Reports p-values and Benjamini-Hochberg corrected p-values.

Author: Greg Gloor, Ruth Grace Wong, Andrew Fernandes, Arianne Albert, Matt Links, Thomas Quinn, 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 1.9.1
In Bioconductor since BioC 3.0 (R-3.1) (2.5 years)
License file LICENSE
Depends methods, stats
Imports BiocParallel, GenomicRanges, IRanges, S4Vectors, SummarizedExperiment, multtest
LinkingTo
Suggests testthat
SystemRequirements
Enhances
URL https://github.com/ggloor/ALDEx2
BugReports https://github.com/ggloor/ALDEx2/issues
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_1.9.1.tar.gz
Windows Binary ALDEx2_1.9.1.zip
Mac OS X 10.11 (El Capitan) ALDEx2_1.9.1.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/ALDEx2
Package Short Url http://bioconductor.org/packages/ALDEx2/
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