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phyloseq in r studio  (RStudio)

 
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    RStudio phyloseq in r studio
    Phyloseq In R Studio, 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/phyloseq+in+r+studio/r+package+phyloseq/10__1029_slash_2023jg007781-146-17-19
    Average 90 stars, based on 1 article reviews
    phyloseq in r studio - by Bioz Stars, 2026-09
    90/100 stars

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    Article Title: Assessing Environmental Quality in a Historically Polluted Fjord: A Comparison of Benthic Foraminiferal eDNA and Morphospecies Approaches
    Article Snippet: Rather than filtering via minimum reads threshold, a rarefaction was applied to the genetic data set using phyloseq in R studio (McMurdie & Holmes, 2013).



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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