ALDEx2
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see ALDEx2.
Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account
Bioconductor version: 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("ALDEx2")):
Installation
To install this package, start R (version "4.4") 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")| ANOVA-Like Differential Expression tool for high throughput sequencing data | HTML | R Script |
| Incorporating Scale Uncertainty into ALDEx2 | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Bayesian, ChIPSeq, DNASeq, DifferentialExpression, GeneExpression, ImmunoOncology, Metagenomics, Microbiome, Posterior p-value, RNASeq, Scale simulation, Sequencing, Software, Transcriptomics |
| Version | 1.36.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (10 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, aIc, ggpicrust2 |
| Suggests Me | dar, pctax |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ALDEx2_1.36.0.tar.gz |
| Windows Binary (x86_64) | ALDEx2_1.36.0.zip |
| macOS Binary (x86_64) | ALDEx2_1.36.0.tgz |
| macOS Binary (arm64) | ALDEx2_1.36.0.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 |