ALDEx2

DOI: 10.18129/B9.bioc.ALDEx2    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see ALDEx2.

Analysis Of Differential Abundance Taking Sample Variation Into Account

Bioconductor version: 3.8

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>

Installation

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

if (!requireNamespace("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")

 

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, ImmunoOncology, Metagenomics, Microbiome, RNASeq, Sequencing, Software
Version	1.14.1
In Bioconductor since	BioC 3.0 (R-3.1) (4.5 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	omicplotR
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	ALDEx2_1.14.1.tar.gz
Windows Binary	ALDEx2_1.14.1.zip
Mac OS X 10.11 (El Capitan)	ALDEx2_1.14.1.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	http://bioconductor.org/packages/ALDEx2/
Package Downloads Report	Download Stats