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ALDEx2

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

Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account


Bioconductor version: Development (3.19)

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 predicted p-values and posterior Benjamini-Hochberg corrected p-values. ALDEx2 also calculates expected standardized effect sizes for paired or unpaired study designs. ALDEx2 can now be used to estimate the effect of scale on the results and report on the scale-dependent robustness of results.

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

Maintainer: Greg Gloor <ggloor at uwo.ca>

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
ANOVA-Like Differential Expression tool for high throughput sequencing data HTML R Script
Incorporating Scale Uncertainty into ALDEx2 HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Bayesian, ChIPSeq, DNASeq, DifferentialExpression, GeneExpression, ImmunoOncology, Metagenomics, Microbiome, Posterior p-value, RNASeq, Scale simulation, Sequencing, Software, Transcriptomics
Version 1.35.0
In Bioconductor since BioC 3.0 (R-3.1) (9.5 years)
License GPL (>=3)
Depends methods, stats, zCompositions, lattice, latticeExtra
Imports Rfast, BiocParallel, GenomicRanges, IRanges, S4Vectors, SummarizedExperiment, multtest, directlabels
System Requirements
URL https://github.com/ggloor/ALDEx_bioc
Bug Reports https://github.com/ggloor/ALDEx_bioc/issues
See More
Suggests testthat, BiocStyle, knitr, rmarkdown, purrr, ggpattern, ggplot2, cowplot, tidyverse, magick
Linking To
Enhances
Depends On Me omicplotR
Imports Me benchdamic, microbiomeMarker
Suggests Me dar
Links To Me
Build Report Build Report

Package Archives

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

Source Package ALDEx2_1.35.0.tar.gz
Windows Binary ALDEx2_1.35.0.zip
macOS Binary (x86_64) ALDEx2_1.35.0.tgz
macOS Binary (arm64) ALDEx2_1.35.0.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