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References
Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L. & Wold, B. Nat. Methods 5, 621–628 (2008).
Trapnell, C. et al. Nat. Biotechnol. 28, 511–515 (2010).
Grabherr, M.G. et al. Nat. Biotechnol. 29, 644–652 (2011).
Gentleman, R.C. et al. Genome Biol. 5, R80 (2004).
Dermitzakis, M., Getz, G., Ardlie, K., Guigo, R. & GTEx Consortium. Bits of DNA https://liorpachter.wordpress.com/author/edermitzakis/. (2013).
Pertea, M. et al. Nat. Biotechnol. 33, 290–295 (2015).
Li, B. & Dewey, C.N. BMC Bioinformatics 12, 323 (2011).
Smyth, G.K. in Bioinformatics and Computational Biology Solutions Using R and Bioconductor (eds. Gentleman, R., Carey, V., Huber, W., Irizarry, R. & Dudoit, S.) 397–420 (Springer, 2005).
Law, C.W., Chen, Y., Shi, W. & Smyth, G.K. Genome Biol. 15, R29 (2014).
Robinson, M.D., McCarthy, D.J. & Smyth, G.K. Bioinformatics 26, 139–140 (2010).
Anders, S. & Huber, W. Genome Biol. 11, R106 (2010).
Chen, Y., McCarthy, D., Robinson, M. & Smyth, G.K. edgeR: differential expression analysis of digital gene expression data User's Guide. http://www.bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf (2011).
Trapnell, C. et al. Nat. Protoc. 7, 562–578 (2012).
Leng, N. et al. Bioinformatics 29, 1035–1043 (2013).
Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Genome Biol. 10, R25 (2009).
Kim, D. et al. Genome Biol. 14, R36 (2013).
Trapnell, C. et al. Nat. Biotechnol. 31, 46–53 (2013).
Lister, R. et al. Science 341, 1237905 (2013).
Young, R.S. et al. Genome Biol. Evol. 4, 427–442 (2012).
Lister, R. et al. Nature 471, 68–73 (2011).
Djebali, S. et al. Nature 489, 101–108 (2012).
Graveley, B.R. et al. Nature 471, 473–479 (2011).
C't Hoen, A.P., Friedländer, M.R. & Almlöf, J. Nature 31, 1015–1022 (2013).
Lappalainen, T. et al. Nature 501, 506–511 (2013).
Storey, J.D. & Tibshirani, R. Proc. Natl. Acad. Sci. USA 100, 9440–9445 (2003).
Frazee, A.C., Sabunciyan, S., Hansen, K.D., Irizarry, R.A. & Leek, J.T. Biostatistics 15, 413–426 (2014).
Kim, S.C. et al. PLoS ONE 8, e55596 (2013).
Yan, L. et al. Nat. Struct. Mol. Biol. 20, 1131–1139 (2013).
Coletta, A., Molter, C., Duqué, R. & Steenhoff, D. Genome Biol. 13, R104 (2012).
Frazee, A.C., Jaffe, A.E., Langmead, B. & Leek, J. bioRxiv http://biorxiv.org/content/biorxiv/early/2014/06/06/006015.full.pdf (2014)
Schroeder, A. et al. BMC Mol. Biol. 7, 3 (2006).
Storey, J.D. et al. PNAS 102, 12837–12842 (2005).
Paulson, J.N., Stine, O.C., Bravo, H.C. & Pop, M. Nat. Methods 10, 1200–1202 (2013).
Price, A.L. et al. Nat. Genet. 38, 904–909 (2006).
Leek, J.T. & Storey, J.D. PLoS Genet. 3, 1724–1735 (2007).
Shabalin, A.A. Bioinformatics 28, 1353–1358 (2012).
Acknowledgements
The authors would like to thank P.A.C. 't Hoen and T. Lappalainen for providing QC data and assistance with contacting ArrayExpress. They would also like to acknowledge C. Trapnell for helpful conversations about Cufflinks architecture and results. J.T.L., G.P. and B.L. were partially supported by US National Institutes of Health 1R01GM105705, and A.C.F. is supported by a Hopkins Sommer Scholarship.
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Frazee, A., Pertea, G., Jaffe, A. et al. Ballgown bridges the gap between transcriptome assembly and expression analysis. Nat Biotechnol 33, 243–246 (2015). https://doi.org/10.1038/nbt.3172
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DOI: https://doi.org/10.1038/nbt.3172
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