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RStudio r package phyloseq
R Package Phyloseq, supplied by RStudio, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/r+package+phyloseq/r+package+phyloseq/pm40594018-265-11-25
Average 90 stars, based on 1 article reviews
r package phyloseq - by Bioz Stars, 2026-11
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Article Title: Winery by-products as a feed source with functional properties: dose–response effect of grape pomace, grape seed meal, and grape seed extract on rumen microbial community and their fermentation activity in RUSITEC
Article Snippet: The rooted tree, taxonomy file, and filtered feature table were used as input to the R package phyloseq [ ] in RStudio (RStudio Team, 2020, Boston, MA, USA).

Article Title: Winery by-products as a feed source with functional properties: dose-response effect of grape pomace, grape seed meal, and grape seed extract on rumen microbial community and their fermentation activity in RUSITEC.
Article Snippet: The rooted tree, taxonomy file, and filtered feature table were used as input to the R package phyloseq [26] in RStudio (RStudio Team, 2020, Boston, MA, USA).

Article Title: Characterization of antibiotic resistance and host-microbiome interactions in the human upper respiratory tract during influenza infection
Article Snippet: The biom file output from QIIME was analyzed in Rstudio [ ] using the phyloseq [ ] R package.

Article Title: Bioactive phenolic compounds from Australian seaweeds and their impact on gut health.
Article Snippet: Alpha and beta diversity analyses were performed using the R package “Phyloseq” (version 1.46)59 on a rarified dataset at 8795 depth (seed = 1997) in RStudio (version 4.3.2)60.

Article Title: No Durable Impact of COVID-19 on Intestinal Disease Activity in Subjects With IBD
Article Snippet: Alpha and beta diversity was calculated using R package “phyloseq,” whereas plots were constructed in “ggplot2.” Beta divergence based on Bray-Curtis dissimilarity was calculated using microbiome package in R studio.

Article Title: Next-generation sequencing reveals predominant bacterial communities during fermentation of Thai fish sauce in large manufacturing plants
Article Snippet: 23 M AN US CR IP T AC CE PT ED ACCEPTED MANUSCRIPT 2 Bacterial communities in fish sauce, at different fermentation phases, from two large 24 manufacturing plants (Factories MC and SQ) in Thailand, were studied.. The bacterial microbiota 25 in a fish sauce mash of > 12 months were examined by 16S rRNA next-generation sequencing.. 26 We revealed the presence of 7 phyla, 14 classes, 21 orders, 31 families, and 45 genera of bacteria 27 in the fish sauce.

Article Title: Function-Based Rhizosphere Assembly along a Gradient of Desiccation in the Former Aral Sea
Article Snippet: The microbial data sets were analyzed with the R package Phyloseq implemented in RStudio ( , ).

Article Title: Impact of land use history on the arbuscular mycorrhizal fungal diversity in arid soils of Argentinean farming fields.
Article Snippet: Finally, taxonomy of AMF OTUs was also refined performing BLAST against the MaarjAM database (https: //maarjam.botany.ut.ee/; Öpik et al. 2010) The two data sets, each one composed of OTU table, taxonomy table and metadata were then imported in Rstudio and were used to create two phyloseq objects with the R package phyloseq (McMurdie and Holmes 2013) that were employed for all the following analyses.



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Primers used in this study for 16S rDNA and ITS2 amplicon <t> sequencing. </t>
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Primers used in this study for 16S rDNA and ITS2 amplicon  sequencing.

Journal: Frontiers in Plant Science

Article Title: The mycoparasite Pythium oligandrum induces legume pathogen resistance and shapes rhizosphere microbiota without impacting mutualistic interactions

doi: 10.3389/fpls.2023.1156733

Figure Lengend Snippet: Primers used in this study for 16S rDNA and ITS2 amplicon sequencing.

Article Snippet: The sequencing data were processed under R v3.4 ( www.r-project.org ) using the R-Studio ( http://www.rstudio.com/ ) Phyloseq package ( ).

Techniques: Amplification, Sequencing

Transcriptomic analysis of Pythium oligandrum -inoculated roots. RNAseq experiments were performed on RNA extracted from in vitro grown plants inoculated with P. oligandrum oospores at different time points. (A) Principal component analysis of data obtained from the RNA sequencing of P. oligandrum and A17 M. truncatula at 3, 5, 7, and 14 days post-inoculation. Orange dots show data belonging to M. truncatula plants inoculated with P. oligandrum , and green dots show data belonging to mock plants. (B) Number of differentially expressed genes (DEGs) at each time point. (C) Venn diagrams representing the DEGs for each condition. (D) Hierarchical clustering on DEGs; clustering was obtained using Hierachical Clustering Explorer version 3.5 with default parameters.

Journal: Frontiers in Plant Science

Article Title: The mycoparasite Pythium oligandrum induces legume pathogen resistance and shapes rhizosphere microbiota without impacting mutualistic interactions

doi: 10.3389/fpls.2023.1156733

Figure Lengend Snippet: Transcriptomic analysis of Pythium oligandrum -inoculated roots. RNAseq experiments were performed on RNA extracted from in vitro grown plants inoculated with P. oligandrum oospores at different time points. (A) Principal component analysis of data obtained from the RNA sequencing of P. oligandrum and A17 M. truncatula at 3, 5, 7, and 14 days post-inoculation. Orange dots show data belonging to M. truncatula plants inoculated with P. oligandrum , and green dots show data belonging to mock plants. (B) Number of differentially expressed genes (DEGs) at each time point. (C) Venn diagrams representing the DEGs for each condition. (D) Hierarchical clustering on DEGs; clustering was obtained using Hierachical Clustering Explorer version 3.5 with default parameters.

Article Snippet: The sequencing data were processed under R v3.4 ( www.r-project.org ) using the R-Studio ( http://www.rstudio.com/ ) Phyloseq package ( ).

Techniques: In Vitro, RNA Sequencing