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pvclust package  (RStudio)

 
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    Structured Review

    RStudio pvclust package
    Comparative analysis of structural characteristics and clustering. ( A ) Clustering analysis of ASA and hydrophobicity: The <t>pvclust</t> package in RStudio was employed for clustering the analysis of residue models based on solvent-accessible surface (ASA) and hydrophobicity. Notably, the models of P.1.4, P.1.8, P.1 and B.1.1.28 exhibit smaller distances on their surfaces, and the model of P.1.7 displays a smaller distance relative to these clusters. In contrast, the P.1.3 and WT-Wuhan models clustered together, distant from the remaining analyzed models. ( B ) Cluster dendrogram of webPIPSA analysis: the webPIPSA analysis of electrostatic surfaces resulted in a cluster dendogram. This analysis reveals the clustering of the S protein from WT-Wuhan with the ancestral B.1.1.28 variant of the Gamma lineage. In contrast, the other variants are grouped together, indicating smaller distances among them. The red boxes indicates the number of clusters we determined for the analysis.
    Pvclust Package, 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/pvclust+package/pvclust+package/pmc11052025-131-16-19
    Average 90 stars, based on 1 article reviews
    pvclust package - by Bioz Stars, 2026-09
    90/100 stars

    Images

    1) Product Images from "A Comparative Analysis of Innate Immune Responses and the Structural Characterization of Spike from SARS-CoV-2 Gamma Variants and Subvariants"

    Article Title: A Comparative Analysis of Innate Immune Responses and the Structural Characterization of Spike from SARS-CoV-2 Gamma Variants and Subvariants

    Journal: Microorganisms

    doi: 10.3390/microorganisms12040720

    Comparative analysis of structural characteristics and clustering. ( A ) Clustering analysis of ASA and hydrophobicity: The pvclust package in RStudio was employed for clustering the analysis of residue models based on solvent-accessible surface (ASA) and hydrophobicity. Notably, the models of P.1.4, P.1.8, P.1 and B.1.1.28 exhibit smaller distances on their surfaces, and the model of P.1.7 displays a smaller distance relative to these clusters. In contrast, the P.1.3 and WT-Wuhan models clustered together, distant from the remaining analyzed models. ( B ) Cluster dendrogram of webPIPSA analysis: the webPIPSA analysis of electrostatic surfaces resulted in a cluster dendogram. This analysis reveals the clustering of the S protein from WT-Wuhan with the ancestral B.1.1.28 variant of the Gamma lineage. In contrast, the other variants are grouped together, indicating smaller distances among them. The red boxes indicates the number of clusters we determined for the analysis.
    Figure Legend Snippet: Comparative analysis of structural characteristics and clustering. ( A ) Clustering analysis of ASA and hydrophobicity: The pvclust package in RStudio was employed for clustering the analysis of residue models based on solvent-accessible surface (ASA) and hydrophobicity. Notably, the models of P.1.4, P.1.8, P.1 and B.1.1.28 exhibit smaller distances on their surfaces, and the model of P.1.7 displays a smaller distance relative to these clusters. In contrast, the P.1.3 and WT-Wuhan models clustered together, distant from the remaining analyzed models. ( B ) Cluster dendrogram of webPIPSA analysis: the webPIPSA analysis of electrostatic surfaces resulted in a cluster dendogram. This analysis reveals the clustering of the S protein from WT-Wuhan with the ancestral B.1.1.28 variant of the Gamma lineage. In contrast, the other variants are grouped together, indicating smaller distances among them. The red boxes indicates the number of clusters we determined for the analysis.

    Techniques Used: Residue, Solvent, Variant Assay

    Related Articles

    Residue:

    Article Title: A Comparative Analysis of Innate Immune Responses and the Structural Characterization of Spike from SARS-CoV-2 Gamma Variants and Subvariants.
    Article Snippet: .. Comparative analysis of structural characteristics and clustering. (A) Clustering analysis of ASA and hydrophobicity: The pvclust package in RStudio was employed for clustering the analysis of residue models based on solvent-accessible surface (ASA) and hydrophobicity. ..

    Solvent:

    Article Title: A Comparative Analysis of Innate Immune Responses and the Structural Characterization of Spike from SARS-CoV-2 Gamma Variants and Subvariants.
    Article Snippet: .. Comparative analysis of structural characteristics and clustering. (A) Clustering analysis of ASA and hydrophobicity: The pvclust package in RStudio was employed for clustering the analysis of residue models based on solvent-accessible surface (ASA) and hydrophobicity. ..

    other:

    Article Title: Tissue-specific mRNA profiling of the Brassica napus-Sclerotinia sclerotiorum interaction uncovers novel regulators of plant immunity.
    Article Snippet: Hierarchical and fuzzy k-means clustering Hierarchical and fuzzy k-means (FKM) clustering was performed using the pvclust (https://cran.r-project.org/web/packages/pvclust/index. html) and cluster (http://cran.r-project.org/web/packages/cluster/ cluster.pdf) packages, respectively, in R studio.

    Article Title: Polyclonal Broadly Neutralizing Antibody Activity Characterized by CD4 Binding Site and V3-Glycan Antibodies in a Subset of HIV-1 Virus Controllers
    Article Snippet: The correlation coefficients and associated p-values were obtained using the cor.test function in R. Hierarchical clustering analysis was performed in R Studio using the pvclust package as previously described ( https://github.com/shimo-lab/pvclust ).

    Article Title: Molecular and morphological characters of Helicotylenchus Steiner, 1945 species from Iran with a note on the identity of H. pseudorobustus (Steiner, 1914) Golden, 1956.
    Article Snippet: Helicotylenchus species were recovered from natural areas of three provinces (Mazandaran, Kerman and Guilan) in Iran, with morphological and molecular characteristics suggesting that they were Helicotylenchus minzi and Helicotylenchus pseudorobustus.. A phylogenetic analysis of the two Helicotylenchus species using 28S rDNA placed H. pseudrobustus and H. minzi in a clade with 1.00 posterior probability.. Results suggest that the Helicotylenchus population identified using molecular characteristics as H. pseudorobustus is a paraphyletic group, with hierarchical clustering analysis indicating a close relationship between the Iranian and the Chinese populations of H. pseudorobustus.

    High Content Screening:

    Article Title: Can the protection be among us? Previous viral contacts and prevalent HLA alleles avoiding an even more disseminated COVID-19 pandemic
    Article Snippet: .. Aiming to verify the alleles frequencies influences in disorder outcomes, and in the pandemic picture, we incorporated them into a Hierarchical Clustering Analysis (HCA) using the pvclust package at the RStudio platform. ..



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    Comparative analysis of structural characteristics and clustering. ( A ) Clustering analysis of ASA and hydrophobicity: The <t>pvclust</t> package in RStudio was employed for clustering the analysis of residue models based on solvent-accessible surface (ASA) and hydrophobicity. Notably, the models of P.1.4, P.1.8, P.1 and B.1.1.28 exhibit smaller distances on their surfaces, and the model of P.1.7 displays a smaller distance relative to these clusters. In contrast, the P.1.3 and WT-Wuhan models clustered together, distant from the remaining analyzed models. ( B ) Cluster dendrogram of webPIPSA analysis: the webPIPSA analysis of electrostatic surfaces resulted in a cluster dendogram. This analysis reveals the clustering of the S protein from WT-Wuhan with the ancestral B.1.1.28 variant of the Gamma lineage. In contrast, the other variants are grouped together, indicating smaller distances among them. The red boxes indicates the number of clusters we determined for the analysis.
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    Comparative analysis of structural characteristics and clustering. ( A ) Clustering analysis of ASA and hydrophobicity: The <t>pvclust</t> package in RStudio was employed for clustering the analysis of residue models based on solvent-accessible surface (ASA) and hydrophobicity. Notably, the models of P.1.4, P.1.8, P.1 and B.1.1.28 exhibit smaller distances on their surfaces, and the model of P.1.7 displays a smaller distance relative to these clusters. In contrast, the P.1.3 and WT-Wuhan models clustered together, distant from the remaining analyzed models. ( B ) Cluster dendrogram of webPIPSA analysis: the webPIPSA analysis of electrostatic surfaces resulted in a cluster dendogram. This analysis reveals the clustering of the S protein from WT-Wuhan with the ancestral B.1.1.28 variant of the Gamma lineage. In contrast, the other variants are grouped together, indicating smaller distances among them. The red boxes indicates the number of clusters we determined for the analysis.
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    Comparative analysis of structural characteristics and clustering. ( A ) Clustering analysis of ASA and hydrophobicity: The <t>pvclust</t> package in RStudio was employed for clustering the analysis of residue models based on solvent-accessible surface (ASA) and hydrophobicity. Notably, the models of P.1.4, P.1.8, P.1 and B.1.1.28 exhibit smaller distances on their surfaces, and the model of P.1.7 displays a smaller distance relative to these clusters. In contrast, the P.1.3 and WT-Wuhan models clustered together, distant from the remaining analyzed models. ( B ) Cluster dendrogram of webPIPSA analysis: the webPIPSA analysis of electrostatic surfaces resulted in a cluster dendogram. This analysis reveals the clustering of the S protein from WT-Wuhan with the ancestral B.1.1.28 variant of the Gamma lineage. In contrast, the other variants are grouped together, indicating smaller distances among them. The red boxes indicates the number of clusters we determined for the analysis.
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    Comparative analysis of structural characteristics and clustering. ( A ) Clustering analysis of ASA and hydrophobicity: The <t>pvclust</t> package in RStudio was employed for clustering the analysis of residue models based on solvent-accessible surface (ASA) and hydrophobicity. Notably, the models of P.1.4, P.1.8, P.1 and B.1.1.28 exhibit smaller distances on their surfaces, and the model of P.1.7 displays a smaller distance relative to these clusters. In contrast, the P.1.3 and WT-Wuhan models clustered together, distant from the remaining analyzed models. ( B ) Cluster dendrogram of webPIPSA analysis: the webPIPSA analysis of electrostatic surfaces resulted in a cluster dendogram. This analysis reveals the clustering of the S protein from WT-Wuhan with the ancestral B.1.1.28 variant of the Gamma lineage. In contrast, the other variants are grouped together, indicating smaller distances among them. The red boxes indicates the number of clusters we determined for the analysis.
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    Image Search Results


    Comparative analysis of structural characteristics and clustering. ( A ) Clustering analysis of ASA and hydrophobicity: The pvclust package in RStudio was employed for clustering the analysis of residue models based on solvent-accessible surface (ASA) and hydrophobicity. Notably, the models of P.1.4, P.1.8, P.1 and B.1.1.28 exhibit smaller distances on their surfaces, and the model of P.1.7 displays a smaller distance relative to these clusters. In contrast, the P.1.3 and WT-Wuhan models clustered together, distant from the remaining analyzed models. ( B ) Cluster dendrogram of webPIPSA analysis: the webPIPSA analysis of electrostatic surfaces resulted in a cluster dendogram. This analysis reveals the clustering of the S protein from WT-Wuhan with the ancestral B.1.1.28 variant of the Gamma lineage. In contrast, the other variants are grouped together, indicating smaller distances among them. The red boxes indicates the number of clusters we determined for the analysis.

    Journal: Microorganisms

    Article Title: A Comparative Analysis of Innate Immune Responses and the Structural Characterization of Spike from SARS-CoV-2 Gamma Variants and Subvariants

    doi: 10.3390/microorganisms12040720

    Figure Lengend Snippet: Comparative analysis of structural characteristics and clustering. ( A ) Clustering analysis of ASA and hydrophobicity: The pvclust package in RStudio was employed for clustering the analysis of residue models based on solvent-accessible surface (ASA) and hydrophobicity. Notably, the models of P.1.4, P.1.8, P.1 and B.1.1.28 exhibit smaller distances on their surfaces, and the model of P.1.7 displays a smaller distance relative to these clusters. In contrast, the P.1.3 and WT-Wuhan models clustered together, distant from the remaining analyzed models. ( B ) Cluster dendrogram of webPIPSA analysis: the webPIPSA analysis of electrostatic surfaces resulted in a cluster dendogram. This analysis reveals the clustering of the S protein from WT-Wuhan with the ancestral B.1.1.28 variant of the Gamma lineage. In contrast, the other variants are grouped together, indicating smaller distances among them. The red boxes indicates the number of clusters we determined for the analysis.

    Article Snippet: The gathered information for each model was subsequently saved, and cluster analysis was performed using the pvclust package within RStudio version 4.2.

    Techniques: Residue, Solvent, Variant Assay