ALDEx2

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see ALDEx2.

Analysis Of Differential Abundance Taking Sample Variation Into Account

Bioconductor version: 3.7

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 (version "3.5") and enter:


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

BiocManager::install("ALDEx2")

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("ALDEx2")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Bayesian, ChIPSeq, DNASeq, DifferentialExpression, GeneExpression, Metagenomics, Microbiome, RNASeq, Sequencing, Software
Version	1.12.0
In Bioconductor since	BioC 3.0 (R-3.1) (9.5 years)
License	file LICENSE
Depends	methods, stats
Imports	BiocParallel, GenomicRanges, IRanges, S4Vectors, SummarizedExperiment, multtest
System Requirements
URL	https://github.com/ggloor/ALDEx2
Bug Reports	https://github.com/ggloor/ALDEx2/issues

Suggests	testthat
Linking To
Enhances
Depends On Me
Imports Me	omicplotR
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	ALDEx2_1.12.0.tar.gz
Windows Binary	ALDEx2_1.12.0.zip
Mac OS X 10.11 (El Capitan)	ALDEx2_1.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ALDEx2
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ALDEx2
Package Short Url	https://bioconductor.org/packages/ALDEx2/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.7	Source Archive