phyloseq protocols

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phyloseq statistics

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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 1.24.2
Stability Stable
R, ade4, ape, Biobase, BiocGenerics, biomformat, Biostrings, cluster, data.table, foreach, ggplot2, igraph, methods, multtest, plyr, reshape2, scales, vegan, BiocStyle, DESeq2, genefilter, knitr, metagenomeSeq, rmarkdown, testthat
Maintained Yes



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  • person_outline Paul J. McMurdie <>

Publication for phyloseq

phyloseq in pipelines

PMCID: 5808123
PMID: 29467733
DOI: 10.3389/fmicb.2018.00102

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

PMCID: 5819220
PMID: 29463295
DOI: 10.1186/s40168-018-0423-6

[…] method. finally, otu tables were produced in a standard biom format for subsequent analyses., all statistical analyses were done using r version 3.3.1 ([], we used the phyloseq r package for community composition analysis [] to infer alpha diversity metrics at the otu level, as well as beta diversity (between sample distance) from the otu table. community […]

PMCID: 5840735
PMID: 29556373
DOI: 10.1186/s12263-018-0594-6

[…] sequences data [] and how erroneous sequences can be detected. due to these challenges, sophisticated pipelines for taxonomic assignment have been developed, like for example qiime [], mothur [], phyloseq [], micca [] and ng-tax [], the latter of which has been developed in our laboratories and provides computationally efficient and accurate taxonomic assignments and quantification of otus […]

PMCID: 5840735
PMID: 29556373
DOI: 10.1186/s12263-018-0594-6

[…] can be projected a posteriori, and their significance can be tested post hoc., several of these statistical tools are standardly embedded in sequence analysis pipelines like mothur [], qiime [] or phyloseq [] and allow to capture measures of alpha- and beta-diversity. choices can be made between default analysis routines and more customized procedures where users can adjust specific settings., […]

PMCID: 5843337
PMID: 29518170
DOI: 10.1371/journal.pone.0194131

[…] analysis, also performed in a pair-wise fashion between samples using bonferroni correction on p-values., data analysis was performed using r statistical software [] with the packages vegan [], phyloseq [] and picante []. furthermore, deseq2 [] was used to highlight otus differentially present among different instars of c. capitata, and when collected from different host fruits., clustering […]

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phyloseq in publications

PMCID: 5952429
PMID: 29764499
DOI: 10.1186/s40168-018-0472-x

[…] plasma glucose level) and 122 postpartum samples (79 and 43 from normoglycaemic and diabetic women, respectively)., alpha diversity metrics (richness and shannon’s index) were calculated using the phyloseq r package based on rarefied otu counts. pielou’s evenness index was calculated as shannon’s index/ln (richness). the cross-sectional difference in alpha diversity between groups […]

PMCID: 5949713
PMID: 29760543
DOI: 10.3748/wjg.v24.i18.1995

[…] using the usearch v9.2.64 package. for otu clustering a threshold of 97% similarity was used through the uparse-otu algorithm. α- and β-diversity analyses were calculated using the r package phyloseq v.1.19.1[] and vegan 2.4_2 packets, using the otu table normalized to the smallest sample size. taxa with differential abundance between groups were identified using the kruskal-wallis test […]

PMCID: 5936483
PMID: 29730829
DOI: 10.1186/s13568-018-0607-2

[…] all graphs were constructed in r using ggplot2., for downstream analysis of the community composition the otu table and taxonomy files generated by mothur, were imported into r and analyzed using phyloseq (mcmurdie and holmes )., the oligotrophic sites were more acidic compared to the mesotrophic sites and contained less dissolved ch4 (see additional file : figure s1). concentrations of nh4+, […]

PMCID: 5938556
PMID: 29765370
DOI: 10.3389/fmicb.2018.00870

[…] reads due to tag-switching as described in ) as a true part of the negative control., diversity estimates (richness and shannon index) were determined using the “estimate_richness” function in phyloseq version 1.16.2 () with r version 3.3.0. significance of the difference in richness between different seasons and location pairs using the wilcoxon rank sum test implemented […]

PMCID: 5934496
PMID: 29755437
DOI: 10.3389/fmicb.2018.00809

[…] each site has between 6 and 12 replicates per time point, for a total of 781 samples., all analyses were performed in r version 3.3.2 (; ). the data were imported into r and divided by site using phyloseq (). all plots were made using ggplot2 (). mantel (999 permutations) and anosim tests were performed in vegan (). correlations between individual taxa and spatiotemporal factors […]

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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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