phyloseq protocols

phyloseq specifications

Information


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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Documentation


Maintainer


  • person_outline Paul J. McMurdie <>

Publication for phyloseq

phyloseq IN pipelines

 (6)
2017
PMCID: 5373524
PMID: 28358811
DOI: 10.1371/journal.pone.0173848

[…] among the abundance of aerobic and anaerobic bacterial taxa present in patients with and without a p/f ratio ≤ 300 (performed in r as anova = lm(taxa_per_seq_count~group, data = ali)) [18]. the phyloseq package within r was used to create a principle components analysis (pca) plot to compare beta diversity across patients [19]. the linear discriminant analysis (lda) effect size (lefse) […]

2017
PMCID: 5479827
PMID: 28638072
DOI: 10.1038/s41598-017-03478-2

[…] hierarchically summed at all taxonomic levels, and the counts were normalized to the relative abundance for each sample. the diversity of the microbial communities was estimated using the r program phyloseq package59. for a deeper analysis of the diversity of the major evolutional clades in the mucosal microbiota, otus were filtered to a relative abundance of at least 1% in at least one sample. […]

2017
PMCID: 5606034
PMID: 28927467
DOI: 10.1186/s40168-017-0341-z

[…] were retained in the further analysis. the selected otus were normalized to the relative abundance for each sample. the diversity of the microbial communities was estimated by using the r program phyloseq package [17]. for a deeper analysis of the diversity of the major evolutional clades in the ruminal microbiota, otus were filtered to acquire a relative abundance of at least 1% in at least […]

2017
PMCID: 5701178
PMID: 29176730
DOI: 10.1038/s41598-017-16353-x

[…] species diversity index shannon-weaver68 was calculated using ‘species’ level of ncbi taxonomy to generate a table with megan 566. permanova and anova statistical analysis were performed with phyloseq.69, as implemented in the tool microbiomeanalyst70. venn diagrams were generated with biovenn71 using the ‘species’ level table as an input to generate area-proportional representation., […]

2016
PMCID: 5098987
PMID: 27853562
DOI: 10.1098/rsos.160471

[…] blast+ identities (c: otu1/otu121/otu162, environmental/clade e: otu4/otu19, symbiodinium1635: otu13/otu124), and their co-occurrence across samples was identified using the tree function in ‘phyloseq’, with the variance-normalized read depth described above. correlations between these otus were calculated with the function ggpairs in the package ‘ggally’ [62]. geometric distances […]

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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