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Bioconductor: open software development for computational biology and bioinformatics.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J. Gentleman RC, et al. Among authors: irizarry r. Genome Biol. 2004;5(10):R80. doi: 10.1186/gb-2004-5-10-r80. Epub 2004 Sep 15. Genome Biol. 2004. PMID: 15461798 Free PMC article.
Experimental design and low-level analysis of microarray data.
Bolstad BM, Collin F, Simpson KM, Irizarry RA, Speed TP. Bolstad BM, et al. Among authors: irizarry ra. Int Rev Neurobiol. 2004;60:25-58. doi: 10.1016/S0074-7742(04)60002-X. Int Rev Neurobiol. 2004. PMID: 15474586 Review. No abstract available.
Top-down standards will not serve systems biology.
Quackenbush J, Stoeckert C, Ball C, Brazma A, Gentleman R, Huber W, Irizarry R, Salit M, Sherlock G, Spellman P, Winegarden N. Quackenbush J, et al. Among authors: irizarry r. Nature. 2006 Mar 2;440(7080):24. doi: 10.1038/440024a. Nature. 2006. PMID: 16511469 No abstract available.
Orchestrating high-throughput genomic analysis with Bioconductor.
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M. Huber W, et al. Among authors: irizarry ra. Nat Methods. 2015 Feb;12(2):115-21. doi: 10.1038/nmeth.3252. Nat Methods. 2015. PMID: 25633503 Free PMC article. Review.
Assessing affymetrix GeneChip microarray quality.
McCall MN, Murakami PN, Lukk M, Huber W, Irizarry RA. McCall MN, et al. BMC Bioinformatics. 2011 May 7;12:137. doi: 10.1186/1471-2105-12-137. BMC Bioinformatics. 2011. PMID: 21548974 Free PMC article.
A benchmark for RNA-seq quantification pipelines.
Teng M, Love MI, Davis CA, Djebali S, Dobin A, Graveley BR, Li S, Mason CE, Olson S, Pervouchine D, Sloan CA, Wei X, Zhan L, Irizarry RA. Teng M, et al. Among authors: irizarry ra. Genome Biol. 2016 Apr 23;17:74. doi: 10.1186/s13059-016-0940-1. Genome Biol. 2016. PMID: 27107712 Free PMC article.
201 results