ALDEx statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Differential expression Normalization chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

ALDEx specifications

Information


Unique identifier OMICS_01297
Name ALDEx
Alternative names ANOVA-Like Differential Expression, ALDEx2
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A table containing per-gene sequencing counts for each replicate and a list indicating which replicate should be grouped in what condition.
Output data It computes one table for all genes containing the following: individual median expression data for each gene in each sample, the median expression for each gene in each condition, the median expression level across conditions (A), the median absolute fold difference, the median effect-size, the median within condition difference and the quantile of zero.
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes

Download


Versioning


Add your version

Documentation


Maintainers


  • person_outline Gregory B. Gloor <>
  • person_outline Thomas Quinn <>

Additional information


https://bioconductor.org/packages/release/bioc/html/ALDEx2.html

Publications for ANOVA-Like Differential Expression

ALDEx in publications

 (24)
PMCID: 5938556
PMID: 29765370
DOI: 10.3389/fmicb.2018.00870

[…] moreover, bacterial taxa previously suggested to contribute to a protective effect had significantly higher relative and absolute abundance in pig stables and farmers’ homes than in suburban homes (aldex2 with p < 0.05), including firmicutes, peptostreptococcaceae, prevotellaceae, lachnospiraceae, ruminococcaceae, ruminiclostridium, and lactobacillus. pig stables had significantly lower […]

PMCID: 5934496
PMID: 29755437
DOI: 10.3389/fmicb.2018.00809

[…] (). all plots were made using ggplot2 (). mantel (999 permutations) and anosim tests were performed in vegan (). correlations between individual taxa and spatiotemporal factors were determined using aldex2 () by the kruskal–wallis test (soil order, land use, and time point) and spearman’s rank correlation (ph) on log-ratio transformed data with 128 monte-carlo permutations. all taxa […]

PMCID: 5865204
PMID: 29572539
DOI: 10.1038/s41598-018-23296-4

[…] extracted into separate tables from the resulting assignment., subsequent processing and analysis was done for each taxonomy level separately according to the gloor coda microbiome tutorial, using aldex2 r package with additions of multivariate generalized linear models for testing the significance of multiple factors and their interactions., the compositional diversity within each sample […]

PMCID: 5770469
PMID: 29339831
DOI: 10.1038/s41598-017-18506-4

[…] spearman’s rank correlation between the relative abundances of each genus (clr transformed) in 128 inferred technical replicates and clr transformed amr relative abundances were calculated with the aldex.corr function from the aldex2 package in r. spearman’s rho values were converted to p-values and corrected by the benjamini-hochberg method. correlations between amr genes were performed […]

PMCID: 5665523
PMID: 29091944
DOI: 10.1371/journal.pone.0187044

[…] were supported by visual inspection of the pcoa plot (). changes in microbial composition at the 97% otu level and at the family-level between surface and homogenized samples were examined using aldex2 [], and no significant differences were found at either taxonomic level, also see . the weak influence of sampling method on community dissimilarity and lack of significant taxonomic shifts […]


To access a full list of publications, you will need to upgrade to our premium service.

ALDEx institution(s)
YouKaryote Genomics, London, ON, Canada; Department of Biochemistry, The University of Western Ontario, London, ON, Canada; Department of Microbiology & Immunology, The University of Western Ontario, London, ON, Canada; Department of Surgery, The University of Western Ontario, London, ON, Canada; Canadian Research & Development Centre for Probiotics, Lawson Health Research Institute, London, ON, Canada
ALDEx funding source(s)
This work was supported by NSERC, CIHR and an Ontario Graduate Scholarship.

ALDEx reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review ALDEx