title: edgeRun: an R package for sensitive, functionally relevant differential expression discovery using an unconditional exact test.
abstract: 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.
authors.affiliation: Department of Biostatistics, Harvard School of Public Health, 655 Huntington Ave, Boston, MA 02115, USA.
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Dimont
authors.affiliation: Department of Biostatistics, Harvard School of Public Health, 655 Huntington Ave, Boston, MA 02115, USA.
authors.forename: Jiantao
authors.initials: J
authors.lastname: Shi
authors.affiliation: Department of Biostatistics, Harvard School of Public Health, 655 Huntington Ave, Boston, MA 02115, USA.
authors.forename: Rory
authors.initials: R
authors.lastname: Kirchner
authors.affiliation: Department of Biostatistics, Harvard School of Public Health, 655 Huntington Ave, Boston, MA 02115, USA, Harvard Stem Cell Institute, 1350 Massachusetts Ave, Cambridge, MA 02138, USA and Sheffield Institute of Translational Neuroscience, University of Sheffield, 385a Glossop Road, Sheffield, S10 2HQ, UK.
authors.forename: Winston
authors.initials: W
authors.lastname: Hide
mesh_terms: D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D020869:Gene Expression Profiling / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008297:Male; D011471:Prostatic Neoplasms / Q000235:genetics*; D012334:RNA, Neoplasm / Q000032:analysis* / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D012334:RNA, Neoplasm