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Waste not, want not: why rarefying microbiome data is inadmissible.
McMurdie PJ, Holmes S. McMurdie PJ, et al. PLoS Comput Biol. 2014 Apr 3;10(4):e1003531. doi: 10.1371/journal.pcbi.1003531. eCollection 2014 Apr. PLoS Comput Biol. 2014. PMID: 24699258 Free PMC article.
Normalization of Microbiome Profiling Data.
McMurdie PJ. McMurdie PJ. Methods Mol Biol. 2018;1849:143-168. doi: 10.1007/978-1-4939-8728-3_10. Methods Mol Biol. 2018. PMID: 30298253
Temporal and spatial variation of the human microbiota during pregnancy.
DiGiulio DB, Callahan BJ, McMurdie PJ, Costello EK, Lyell DJ, Robaczewska A, Sun CL, Goltsman DS, Wong RJ, Shaw G, Stevenson DK, Holmes SP, Relman DA. DiGiulio DB, et al. Among authors: mcmurdie pj. Proc Natl Acad Sci U S A. 2015 Sep 1;112(35):11060-5. doi: 10.1073/pnas.1502875112. Epub 2015 Aug 17. Proc Natl Acad Sci U S A. 2015. PMID: 26283357 Free PMC article.
DADA2: High-resolution sample inference from Illumina amplicon data.
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP. Callahan BJ, et al. Among authors: mcmurdie pj. Nat Methods. 2016 Jul;13(7):581-3. doi: 10.1038/nmeth.3869. Epub 2016 May 23. Nat Methods. 2016. PMID: 27214047 Free PMC article.
[No authors listed] [No authors listed] PMID: 27847586
Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses.
Callahan BJ, Sankaran K, Fukuyama JA, McMurdie PJ, Holmes SP. Callahan BJ, et al. Among authors: mcmurdie pj. F1000Res. 2016 Jun 24;5:1492. doi: 10.12688/f1000research.8986.2. eCollection 2016. F1000Res. 2016. PMID: 27508062 Free PMC article.
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