phyloseq specifications


Unique identifier OMICS_01520
Name phyloseq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU Affero General Public License version 3
Computer skills Advanced
Version 1.16.2
Stability Stable
Maintained Yes


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  • person_outline Paul J. McMurdie <>

phyloseq article

phyloseq citations

PMCID: 5808123

[…] and the beta diversity among the samples was measured using weighted unifrac (lozupone and knight, 2005) metric. taxonomic composition, and diversity results were visualized using the r package phyloseq v.1.14.0 (mcmurdie and holmes, 2013). blastn (basic local alignment search tool) searches against the ncbi (national center for biotechnology information) database of nucleotides (nt) […]

PMCID: 4947590

[…] e-value ≤1e - 5, identity ≥60%, and alignment length ≥15 base pairs., after annotation, biological replicates were pooled by treatment, and analyzed in r (r development core team, 2011), using the phyloseq (mcmurdie and holmes, 2013) and deseq2 (love et al., 2014) packages. differences in the abundance of taxa and the variance in expression of transcripts were characterized using the deseq2 […]

PMCID: 4849429

[…] derived from greengenes, rdpii and ncbi. sequence data of this study is submitted in the ncbi under project no. prjna300497., the otu biodiversity and richness were calculated using r package phyloseq (1.7.24) implemented with non-parametric chao1 and rarefaction analysis that showed the uniformity and distribution of otus in different groups (mcmurdie and holmes, 2012). r package “rich” […]

phyloseq institution(s)
Department of Statistics, Stanford University, Stanford, CA, USA; The Roslin Institute, University of Edinburgh, UK
phyloseq funding source(s)
This work was supported by grant NIH-R01GM086884.

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