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wgcna r package  (RStudio)

 
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    RStudio wgcna r package
    Wgcna R 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/r+package+wgcna/r+package+wgcna/pm40199341-58-10-14
    Average 90 stars, based on 1 article reviews
    wgcna r package - by Bioz Stars, 2026-09
    90/100 stars

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    Related Articles

    other:

    Article Title: iTRAQ-based proteomic analysis reveals the effect of ribosomal proteins on essential-oil accumulation in Houttuynia cordata Thunb.
    Article Snippet: The Weighted Gene CoExpression Network Analysisn (WGCNA) of identified proteins was performed with the R package WGCNA ( https://cran.rstudio.com/web/packages/WGCNA ), and further bioinformatic analysis of DEP was performed using the OECloud tools ( https://cloud.oebiotech.cn/ ), based on the Gene Ontology (GO) categories and KEGG Ortholog database.

    Article Title: Multi-factor mediated functional modules identify novel classification of ulcerative colitis and functional gene panel
    Article Snippet: WGCNA of UC-related genes was performed using the R package WGCNA ( https://cran.rstudio.com/web/packages/WGCNA/ ).

    Construct:

    Article Title: Identification and expression profiles of xylogen-like arabinogalactan protein (XYLP) gene family in Phyllostachys edulis in different developmental tissues and under various abiotic stresses.
    Article Snippet: Xylogen-like arabinogalactan protein (XYLP) is an atypical lipid transport protein.. In this study, 23 Phyllostachys edulis XYLPs were identified, and their proteins contain characteristic structures of AGP and nsLTP domain.. All PeXYLPs can be divided into four clades, and their genes were unevenly distributed on 11 chromosome scaffolds.

    Expressing:

    Article Title: Identification and expression profiles of xylogen-like arabinogalactan protein (XYLP) gene family in Phyllostachys edulis in different developmental tissues and under various abiotic stresses.
    Article Snippet: Xylogen-like arabinogalactan protein (XYLP) is an atypical lipid transport protein.. In this study, 23 Phyllostachys edulis XYLPs were identified, and their proteins contain characteristic structures of AGP and nsLTP domain.. All PeXYLPs can be divided into four clades, and their genes were unevenly distributed on 11 chromosome scaffolds.

    Gene Expression:

    Article Title: Identification of hub genes and key modules in laryngeal squamous cell carcinoma
    Article Snippet: .. R package WGCNA ( ) in RStudio were used to carry out WGCNA for the LSCC gene expression data in TCGA and GEO databases. ..



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    wgcna r package  (RStudio)
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    https://www.bioz.com/product/r+package+wgcna/r+package+wgcna/pm40199341-58-10-14
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    r package wgcna  (RStudio)
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    Semi-quantitative protein expression and multivariate analysis of eigen-protein expression. (A) Volcano plots of protein expression in SPA vs . LPA. (B) Expressions of HLA class I proteins, HLA-G and HLA-B, are presented in all the sample tissues. (C) An ANOVA test of HLA-G expressions among three subtypes. (D) Multivariate correlation analysis (MVA) for the spectral counting-based expression of forty eigen-protein and fifteen proteins characteristic of the respective subtypes, assuming three-group clustering (correlation coefficient: Pearson; heatmap order: hierarchical clustering; agglomeration method: complete; the number of clusters: 3). The eighteen eigen-proteins of the <t>WGCNA</t> modules relatively well correlated ( r > 0.4) with and upregulated proteins characteristic of respective subtypes are denoted in colored filled-circles and colored circles (LPA: red; MPA: blue; SPA: green).
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    wgcna r package  (BioCloud Inc)
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    Semi-quantitative protein expression and multivariate analysis of eigen-protein expression. (A) Volcano plots of protein expression in SPA vs . LPA. (B) Expressions of HLA class I proteins, HLA-G and HLA-B, are presented in all the sample tissues. (C) An ANOVA test of HLA-G expressions among three subtypes. (D) Multivariate correlation analysis (MVA) for the spectral counting-based expression of forty eigen-protein and fifteen proteins characteristic of the respective subtypes, assuming three-group clustering (correlation coefficient: Pearson; heatmap order: hierarchical clustering; agglomeration method: complete; the number of clusters: 3). The eighteen eigen-proteins of the <t>WGCNA</t> modules relatively well correlated ( r > 0.4) with and upregulated proteins characteristic of respective subtypes are denoted in colored filled-circles and colored circles (LPA: red; MPA: blue; SPA: green).
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    r studio package wgcna  (RStudio)
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    Semi-quantitative protein expression and multivariate analysis of eigen-protein expression. (A) Volcano plots of protein expression in SPA vs . LPA. (B) Expressions of HLA class I proteins, HLA-G and HLA-B, are presented in all the sample tissues. (C) An ANOVA test of HLA-G expressions among three subtypes. (D) Multivariate correlation analysis (MVA) for the spectral counting-based expression of forty eigen-protein and fifteen proteins characteristic of the respective subtypes, assuming three-group clustering (correlation coefficient: Pearson; heatmap order: hierarchical clustering; agglomeration method: complete; the number of clusters: 3). The eighteen eigen-proteins of the <t>WGCNA</t> modules relatively well correlated ( r > 0.4) with and upregulated proteins characteristic of respective subtypes are denoted in colored filled-circles and colored circles (LPA: red; MPA: blue; SPA: green).
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    wgcna package r-package v.3.1.1  (RStudio)
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    RStudio wgcna package r-package v.3.1.1
    Semi-quantitative protein expression and multivariate analysis of eigen-protein expression. (A) Volcano plots of protein expression in SPA vs . LPA. (B) Expressions of HLA class I proteins, HLA-G and HLA-B, are presented in all the sample tissues. (C) An ANOVA test of HLA-G expressions among three subtypes. (D) Multivariate correlation analysis (MVA) for the spectral counting-based expression of forty eigen-protein and fifteen proteins characteristic of the respective subtypes, assuming three-group clustering (correlation coefficient: Pearson; heatmap order: hierarchical clustering; agglomeration method: complete; the number of clusters: 3). The eighteen eigen-proteins of the <t>WGCNA</t> modules relatively well correlated ( r > 0.4) with and upregulated proteins characteristic of respective subtypes are denoted in colored filled-circles and colored circles (LPA: red; MPA: blue; SPA: green).
    Wgcna Package R Package V.3.1.1, 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
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    Image Search Results


    Semi-quantitative protein expression and multivariate analysis of eigen-protein expression. (A) Volcano plots of protein expression in SPA vs . LPA. (B) Expressions of HLA class I proteins, HLA-G and HLA-B, are presented in all the sample tissues. (C) An ANOVA test of HLA-G expressions among three subtypes. (D) Multivariate correlation analysis (MVA) for the spectral counting-based expression of forty eigen-protein and fifteen proteins characteristic of the respective subtypes, assuming three-group clustering (correlation coefficient: Pearson; heatmap order: hierarchical clustering; agglomeration method: complete; the number of clusters: 3). The eighteen eigen-proteins of the WGCNA modules relatively well correlated ( r > 0.4) with and upregulated proteins characteristic of respective subtypes are denoted in colored filled-circles and colored circles (LPA: red; MPA: blue; SPA: green).

    Journal: Frontiers in Oncology

    Article Title: Cancer cell immunity-related protein co-expression networks are associated with early-stage solid-predominant lung adenocarcinoma

    doi: 10.3389/fonc.2024.1273780

    Figure Lengend Snippet: Semi-quantitative protein expression and multivariate analysis of eigen-protein expression. (A) Volcano plots of protein expression in SPA vs . LPA. (B) Expressions of HLA class I proteins, HLA-G and HLA-B, are presented in all the sample tissues. (C) An ANOVA test of HLA-G expressions among three subtypes. (D) Multivariate correlation analysis (MVA) for the spectral counting-based expression of forty eigen-protein and fifteen proteins characteristic of the respective subtypes, assuming three-group clustering (correlation coefficient: Pearson; heatmap order: hierarchical clustering; agglomeration method: complete; the number of clusters: 3). The eighteen eigen-proteins of the WGCNA modules relatively well correlated ( r > 0.4) with and upregulated proteins characteristic of respective subtypes are denoted in colored filled-circles and colored circles (LPA: red; MPA: blue; SPA: green).

    Article Snippet: The WGCNA analysis was performed using the WGCNA R-package ( ) implemented in RStudio.

    Techniques: Expressing

    The forty protein network modules identified by weighted gene co-expression network analysis (WGCNA). (A) Sample dendrogram and trait heatmap, (B) protein cluster dendrogram, and (C) pairwise correlations between the 40 identified modules concerning the connectivity measure (KME) of the module eigen-protein (correlation coefficient: Pearson; heatmap order: Euclidean; agglomeration method: complete; the number of clusters: 3), where the color bars represent the three clusters, together with lists of module ID, module color and eigen-protein.

    Journal: Frontiers in Oncology

    Article Title: Cancer cell immunity-related protein co-expression networks are associated with early-stage solid-predominant lung adenocarcinoma

    doi: 10.3389/fonc.2024.1273780

    Figure Lengend Snippet: The forty protein network modules identified by weighted gene co-expression network analysis (WGCNA). (A) Sample dendrogram and trait heatmap, (B) protein cluster dendrogram, and (C) pairwise correlations between the 40 identified modules concerning the connectivity measure (KME) of the module eigen-protein (correlation coefficient: Pearson; heatmap order: Euclidean; agglomeration method: complete; the number of clusters: 3), where the color bars represent the three clusters, together with lists of module ID, module color and eigen-protein.

    Article Snippet: The WGCNA analysis was performed using the WGCNA R-package ( ) implemented in RStudio.

    Techniques: Expressing

    Relationship between module eigen-proteins and the clinical traits of three subtypes LPA, MPA, and SPA. Each row in the embedded table represents weighted gene co-expression network analysis results for each module. The first and second columns in the table represent the module identification and color name of a module, respectively. The third column represents the number of proteins in each module. The table is color-coded by the correlation coefficient, in which the intensity and direction of the correlations are indicated (red, positive correlation; blue, negative correlation). The seventh to ninth columns present the p -values of the correlation coefficients, and the tenth to thirteenth columns are q -values by multiple testing correction using the Benjamini–Hochberg method, where significant p -value (<0.05) and q -values (< 0.1) are highlighted in bright red background. p -values between 0.05 and 0.1 are highlighted in yellow background. The fourteenth to sixteenth columns present a number of overlaps between module proteins and proteins upregulated in each subtype. The eighteenth to twenty-one columns present results of the statistical over-representative analysis (ORA) using the hypergeometric overlapping test of all the WGCNA modules with proteins upregulated (more than twice) uniquely for the individual subtypes: 397 proteins in LPA, 314 in MPA, and 474 in SPA, where the Benjamini–Hochberg corrected significant q -values (< 0.05) are highlighted in bright red background.

    Journal: Frontiers in Oncology

    Article Title: Cancer cell immunity-related protein co-expression networks are associated with early-stage solid-predominant lung adenocarcinoma

    doi: 10.3389/fonc.2024.1273780

    Figure Lengend Snippet: Relationship between module eigen-proteins and the clinical traits of three subtypes LPA, MPA, and SPA. Each row in the embedded table represents weighted gene co-expression network analysis results for each module. The first and second columns in the table represent the module identification and color name of a module, respectively. The third column represents the number of proteins in each module. The table is color-coded by the correlation coefficient, in which the intensity and direction of the correlations are indicated (red, positive correlation; blue, negative correlation). The seventh to ninth columns present the p -values of the correlation coefficients, and the tenth to thirteenth columns are q -values by multiple testing correction using the Benjamini–Hochberg method, where significant p -value (<0.05) and q -values (< 0.1) are highlighted in bright red background. p -values between 0.05 and 0.1 are highlighted in yellow background. The fourteenth to sixteenth columns present a number of overlaps between module proteins and proteins upregulated in each subtype. The eighteenth to twenty-one columns present results of the statistical over-representative analysis (ORA) using the hypergeometric overlapping test of all the WGCNA modules with proteins upregulated (more than twice) uniquely for the individual subtypes: 397 proteins in LPA, 314 in MPA, and 474 in SPA, where the Benjamini–Hochberg corrected significant q -values (< 0.05) are highlighted in bright red background.

    Article Snippet: The WGCNA analysis was performed using the WGCNA R-package ( ) implemented in RStudio.

    Techniques: Expressing

    Bubble charts of the canonical pathways significant to the WGCNA modules obtained by IPA. (A) the WM1 (pink) network module; (B) the WM2 (turquoise) network module.

    Journal: Frontiers in Oncology

    Article Title: Cancer cell immunity-related protein co-expression networks are associated with early-stage solid-predominant lung adenocarcinoma

    doi: 10.3389/fonc.2024.1273780

    Figure Lengend Snippet: Bubble charts of the canonical pathways significant to the WGCNA modules obtained by IPA. (A) the WM1 (pink) network module; (B) the WM2 (turquoise) network module.

    Article Snippet: The WGCNA analysis was performed using the WGCNA R-package ( ) implemented in RStudio.

    Techniques: