Jaffe AE - Search Results

1

recount3: summaries and queries for large-scale RNA-seq expression and splicing.

Wilks C, Zheng SC, Chen FY, Charles R, Solomon B, Ling JP, Imada EL, Zhang D, Joseph L, Leek JT, Jaffe AE, Nellore A, Collado-Torres L, Hansen KD, Langmead B. Wilks C, et al. Among authors: jaffe ae. Genome Biol. 2021 Nov 29;22(1):323. doi: 10.1186/s13059-021-02533-6. Genome Biol. 2021. PMID: 34844637 Free PMC article.

2

Significance analysis and statistical dissection of variably methylated regions.

Jaffe AE, Feinberg AP, Irizarry RA, Leek JT. Jaffe AE, et al. Biostatistics. 2012 Jan;13(1):166-78. doi: 10.1093/biostatistics/kxr013. Epub 2011 Jun 17. Biostatistics. 2012. PMID: 21685414 Free PMC article.

3

The sva package for removing batch effects and other unwanted variation in high-throughput experiments.

Leek JT, Johnson WE, Parker HS, Jaffe AE, Storey JD. Leek JT, et al. Among authors: jaffe ae. Bioinformatics. 2012 Mar 15;28(6):882-3. doi: 10.1093/bioinformatics/bts034. Epub 2012 Jan 17. Bioinformatics. 2012. PMID: 22257669 Free PMC article.

4

Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies.

Jaffe AE, Murakami P, Lee H, Leek JT, Fallin MD, Feinberg AP, Irizarry RA. Jaffe AE, et al. Int J Epidemiol. 2012 Feb;41(1):200-9. doi: 10.1093/ije/dyr238. Int J Epidemiol. 2012. PMID: 22422453 Free PMC article.

5

Gene set bagging for estimating the probability a statistically significant result will replicate.

Jaffe AE, Storey JD, Ji H, Leek JT. Jaffe AE, et al. BMC Bioinformatics. 2013 Dec 12;14:360. doi: 10.1186/1471-2105-14-360. BMC Bioinformatics. 2013. PMID: 24330332 Free PMC article.

6

Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays.

Aryee MJ, Jaffe AE, Corrada-Bravo H, Ladd-Acosta C, Feinberg AP, Hansen KD, Irizarry RA. Aryee MJ, et al. Among authors: jaffe ae. Bioinformatics. 2014 May 15;30(10):1363-9. doi: 10.1093/bioinformatics/btu049. Epub 2014 Jan 28. Bioinformatics. 2014. PMID: 24478339 Free PMC article.

7

Developmental regulation of human cortex transcription and its clinical relevance at single base resolution.

Jaffe AE, Shin J, Collado-Torres L, Leek JT, Tao R, Li C, Gao Y, Jia Y, Maher BJ, Hyde TM, Kleinman JE, Weinberger DR. Jaffe AE, et al. Nat Neurosci. 2015 Jan;18(1):154-161. doi: 10.1038/nn.3898. Epub 2014 Dec 15. Nat Neurosci. 2015. PMID: 25501035 Free PMC article.

8

Ballgown bridges the gap between transcriptome assembly and expression analysis.

Frazee AC, Pertea G, Jaffe AE, Langmead B, Salzberg SL, Leek JT. Frazee AC, et al. Among authors: jaffe ae. Nat Biotechnol. 2015 Mar;33(3):243-6. doi: 10.1038/nbt.3172. Nat Biotechnol. 2015. PMID: 25748911 Free PMC article. No abstract available.

9

Polyester: simulating RNA-seq datasets with differential transcript expression.

Frazee AC, Jaffe AE, Langmead B, Leek JT. Frazee AC, et al. Among authors: jaffe ae. Bioinformatics. 2015 Sep 1;31(17):2778-84. doi: 10.1093/bioinformatics/btv272. Epub 2015 Apr 28. Bioinformatics. 2015. PMID: 25926345 Free PMC article.

10

Practical impacts of genomic data "cleaning" on biological discovery using surrogate variable analysis.

Jaffe AE, Hyde T, Kleinman J, Weinbergern DR, Chenoweth JG, McKay RD, Leek JT, Colantuoni C. Jaffe AE, et al. BMC Bioinformatics. 2015 Nov 6;16:372. doi: 10.1186/s12859-015-0808-5. BMC Bioinformatics. 2015. PMID: 26545828 Free PMC article.

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