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phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data.
McMurdie PJ, Holmes S. McMurdie PJ, et al. PLoS One. 2013 Apr 22;8(4):e61217. doi: 10.1371/journal.pone.0061217. Print 2013. PLoS One. 2013. PMID: 23630581 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
Localized plasticity in the streamlined genomes of vinyl chloride respiring Dehalococcoides.
McMurdie PJ, Behrens SF, Müller JA, Göke J, Ritalahti KM, Wagner R, Goltsman E, Lapidus A, Holmes S, Löffler FE, Spormann AM. McMurdie PJ, et al. PLoS Genet. 2009 Nov;5(11):e1000714. doi: 10.1371/journal.pgen.1000714. Epub 2009 Nov 6. PLoS Genet. 2009. PMID: 19893622 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.
Shiny-phyloseq: Web application for interactive microbiome analysis with provenance tracking.
McMurdie PJ, Holmes S. McMurdie PJ, et al. Bioinformatics. 2015 Jan 15;31(2):282-3. doi: 10.1093/bioinformatics/btu616. Epub 2014 Sep 26. Bioinformatics. 2015. PMID: 25262154 Free PMC article.
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.
Comparisons of distance methods for combining covariates and abundances in microbiome studies.
Fukuyama J, McMurdie PJ, Dethlefsen L, Relman DA, Holmes S. Fukuyama J, et al. Among authors: mcmurdie pj. Pac Symp Biocomput. 2012:213-24. Pac Symp Biocomput. 2012. PMID: 22174277 Free PMC article.
Phyloseq: a bioconductor package for handling and analysis of high-throughput phylogenetic sequence data.
McMurdie PJ, Holmes S. McMurdie PJ, et al. Pac Symp Biocomput. 2012:235-46. Pac Symp Biocomput. 2012. PMID: 22174279 Free PMC article.
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