Enables timecourse and multi-group analyses • Can adjust for confounders or batch effects • Runs in seconds: on cancer data set, 0.7 sec; Cuffdiff: 10 hours and EBSeq: 6 hours EBSeq: Leng et al, Bioinformatics 2013
(2014). “Differential expression analysis of RNA-seq data at single-base resolution.” Biostatistics 15(3): 413-426 Frazee AC, Pertea G, Jaffe AE, Salzberg SL, Leek JT (2015). “Ballgown bridges the gap between transcriptome assembly and expression analysis.” Nature Biotechnology, to appear. AC’t Hoen P et al (2013): “Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories.” Nature Biotechnology 31(11): 1015-22. Anders S and Huber W (2010). “Differential expression analysis for sequence count data.” Genome Biology 11(10): R106. Bernard E, Jacob L, Mairal J, Vert J (2014). “Efficient RNA isoform identification and quantification from RNA-seq data with network flows.” Bioinformatics 30(17): 2447-2455. Efron B (2008): “Microarrays, empirical Bayes, and the two-groups model.” Statistical Science 23(1): 1-22. Jaffe AE, Murakami P, Lee H, Leek JT, Fallin MD, Feinberg AP, Irizarry RA (2012): “Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies.” International Journal of Epidemiology 41(1): 200-209. Lappalainen T et al (2013). “Transcriptome and genome sequencing uncovers functional variation in humans.” Nature 501(7468): 506-11. Leng N, Dawson JA, Thomson JA, Ruotti V, Rissman AI, Smits BMG, Haag JD, Gould MN, Steward RM, Kendziorski C (2013). “EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments.” Bioinformatics 29(8): 1035-1043. Robinson MD, McCarthy DJ, Smyth GK (2010). “edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.” Bioinformatics 26(1): 139-40. Smyth GK (2004). Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology 3(1):3. Trapnell C, Hendrickson DG, Sauvageau M, Goff L, Rinn JL, Pachter L (2013). “Differential analysis of gene regulation at transcript resolution with RNA-seq.” Nature Biotechnology 31(1): 46-53. References
[preprint link] • Polyester: BiorXiv [preprint link] • ReCount: BMC Bioinformatics [link] • RNA-seq book chapter: [link, Chapter 6] Software https://github.com/alyssafrazee • Ballgown: [link][dev link] • Polyester: [link][dev link] • DER Finder (Leonardo Collado Torres): [link] Where to find my work These links, plus side projects and blog posts: alyssafrazee.com
alyssafrazee
digitalnaturegroup
kei18
koheishinden
eumesy
anugrahsr
lancers_pr
tkym1220
mkimura
masakat0
daigo0927
trycycle
reverentgeek
mthomps
carmenhchung
cherdarchuk
samlambert
cassininazir
robhawkes
qrush
geeforr
revolveconf
ufuk
keithpitt
![Papers • DER Finder: Biostatistics [link] • Ballgown: Nature Biotechnology](https://files.speakerdeck.com/presentations/a4e00c8069660132c64e7aad183d1e28/slide_56.jpg){kind=link}
![• human diversity: Simon Abrams, CC BY-SA 2.0 [link] •](https://files.speakerdeck.com/presentations/a4e00c8069660132c64e7aad183d1e28/slide_57.jpg){kind=link}
