ALDEx2

DOI: 10.18129/B9.bioc.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 (3.9)

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.

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

Maintainer: Greg Gloor <ggloor at uwo.ca>

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

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("ALDEx2", version = "3.9")

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

Details

biocViews Bayesian, ChIPSeq, DNASeq, DifferentialExpression, GeneExpression, ImmunoOncology, Metagenomics, Microbiome, RNASeq, Sequencing, Software, Transcriptomics
Version 1.15.2
In Bioconductor since BioC 3.0 (R-3.1) (4 years)
License file LICENSE
Depends methods, stats
Imports BiocParallel, GenomicRanges, IRanges, S4Vectors, SummarizedExperiment, multtest
LinkingTo
Suggests testthat, BiocStyle, knitr, rmarkdown
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_1.15.2.tar.gz
Windows Binary ALDEx2_1.15.2.zip
Mac OS X 10.11 (El Capitan) ALDEx2_1.15.2.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

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