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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
biochemistry, genetics and molecular biology
EdgeRun: An R package for sensitive, functionally relevant differential expression discovery using an unconditional exact test
Bioinformatics, Volume 31, No. 15, Year 2015
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Description
Next-generation sequencing platforms for measuring digital expression such as RNA-Seq are displacing traditional microarray-based methods in biological experiments. The detection of differentially expressed genes between groups of biological conditions has led to the development of numerous bioinformatics tools, but so far, few exploit the expanded dynamic range afforded by the new technologies. We present edgeRun, an R package that implements an unconditional exact test that is a more powerful version of the exact test in edgeR. This increase in power is especially pronounced for experiments with as few as two replicates per condition, for genes with low total expression and with large biological coefficient of variation. In comparison with a panel of other tools, edgeRun consistently captures functionally similar differentially expressed genes. © The Author 2015. Published by Oxford University Press.
Authors & Co-Authors
Dimont, Emmanuel
United States, Boston
Harvard T.h. Chan School of Public Health
Hide, Winston A.
United States, Boston
Harvard T.h. Chan School of Public Health
United States, Cambridge
Harvard Stem Cell Institute
United Kingdom, Sheffield
The University of Sheffield
Statistics
Citations: 39
Authors: 2
Affiliations: 3
Identifiers
Doi:
10.1093/bioinformatics/btv209
ISSN:
13674803