- Unique identifier:
- Alternative name:
- Command line interface
- Input data:
- A table containing per-gene sequencing counts for each replicate and a list indicating which replicate should be grouped in what condition.
- Operating system:
- Unix/Linux, Mac OS, Windows
- GNU General Public License version 3.0
- ANOVA-Like Differential Expression
- Software type:
- Restrictions to use:
- 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.
- Programming languages:
- Computer skills:
- Gregory B. Gloor <>
- Thomas Quinn <>
No open topic.
(Fernandes et al., 2013)
ANOVA-like differential expression (ALDEx) analysis for mixed population RNA-Seq.
PMID: 23843979 DOI: 10.1371/journal.pone.0067019
(Fernandes et al., 2014)
Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis.
PMID: 24910773 DOI: 10.1186/2049-2618-2-15
(Quinn et al., 2017)
Differential expression analysis of log-ratio transformed counts: benchmarking methods for RNA-Seq data.
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
This work was supported by NSERC, CIHR and an Ontario Graduate Scholarship.
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