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>
citation("ALDEx2")):
Installation
To install this package, start R (version "3.5") 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")| An R Package for determining differential abundance in high throughput sequencing experiments | R Script | |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
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) (9.5 years) |
| License | file LICENSE |
| Depends | methods, stats |
| Imports | BiocParallel, GenomicRanges, IRanges, S4Vectors, SummarizedExperiment, multtest |
| System Requirements | |
| URL | https://github.com/ggloor/ALDEx2 |
| Bug Reports | https://github.com/ggloor/ALDEx2/issues |
See More
| Suggests | testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | omicplotR |
| Suggests Me | |
| Links To Me | |
| Build Report | 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/ALDEx2/ |
| Package Short Url | https://bioconductor.org/packages/ALDEx2/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.8 | Source Archive |