ALDEx2

DOI: 10.18129/B9.bioc.ALDEx2  

Analysis Of Differential Abundance Taking Sample Variation Into Account

Bioconductor version: Release (3.16)

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 Wilcoxon Rank Sum test and Welch's t-test (via aldex.ttest), a Kruskal-Wallis test (via aldex.kw), a generalized linear model (via aldex.glm), or a correlation test (via aldex.corr). All tests report p-values and Benjamini-Hochberg corrected p-values. ALDEx2 also calculates expected standardized effect sizes for paired or unpaired study designs.

Author: Greg Gloor, Andrew Fernandes, Jean Macklaim, Arianne Albert, Matt Links, Thomas Quinn, Jia Rong Wu, Ruth Grace Wong, Brandon Lieng

Maintainer: Greg Gloor <ggloor at uwo.ca>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	ANOVA-Like Differential Expression tool for high throughput sequencing data
PDF		Reference Manual
Text		NEWS

Details

biocViews	Bayesian, ChIPSeq, DNASeq, DifferentialExpression, GeneExpression, ImmunoOncology, Metagenomics, Microbiome, RNASeq, Sequencing, Software, Transcriptomics
Version	1.30.0
In Bioconductor since	BioC 3.0 (R-3.1) (8.5 years)
License	GPL (>= 3)
Depends	methods, stats, zCompositions
Imports	Rfast, BiocParallel, GenomicRanges, IRanges, S4Vectors, SummarizedExperiment, multtest
LinkingTo
Suggests	testthat, BiocStyle, knitr, rmarkdown
SystemRequirements
Enhances
URL	https://github.com/ggloor/ALDEx_bioc
BugReports	https://github.com/ggloor/ALDEx_bioc/issues
Depends On Me	omicplotR
Imports Me	benchdamic, microbiomeMarker
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	ALDEx2_1.30.0.tar.gz
Windows Binary	ALDEx2_1.30.0.zip
macOS Binary (x86_64)	ALDEx2_1.30.0.tgz
macOS Binary (arm64)	ALDEx2_1.30.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ALDEx2
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ALDEx2
Bioc Package Browser	https://code.bioconductor.org/browse/ALDEx2/
Package Short Url	https://bioconductor.org/packages/ALDEx2/
Package Downloads Report	Download Stats