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R statistical platform

R is an open-source software environment for statistical computing and graphics. It provides a wide variety of statistical and graphical techniques, including linear and nonlinear modeling, classical statistical tests, time-series analysis, classification, clustering, and others. R is widely used in academic and research communities for data analysis and visualization.

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Lab products found in correlation

8 protocols using r statistical platform

1

Genome-Wide Association Analysis

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Statistical analysis was conducted with the R statistical platform (http://cran.r-project.org) using the package SNPassoc (SNPs-based whole-genome association studies. R package version 1.9-2. https://CRAN.R-project.org/package=SNPassoc). In the analysis of single SNPs, multiple inheritance models were used: Co-dominant, dominant, and recessive. Analysis of gene–gene interactions was carried out for the dominant and recessive models. Inheritance models were created with respect to minor alleles. The significance of interactions was calculated by comparing two models with and without the interaction term, using likelihood ratio tests. p < 0.05 was considered statistically significant.
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2

Statistical Analysis of Genetic Determinants

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All statistical analyses were performed using GraphPad Prism software version 8.0 (GRAPH PAD Software Inc, San Diego, CA, USA). To determine the relationship between phenotypic and genetic determinants, the chi-square Pearson test was used. All correlation analyses were calculated using Pearson correlation. The occurrence of genes was marked as “1” when the gene was present, and “0” when it was absent, in which case the results of the Pearson correlation are identical to the point–biserial correlation. Results were considered statistically significant at p < 0.05. The R statistical platform (https://www.r-project.org) (accessed on 13 September 2022) and RStudio program (https://rstudio.com/) (accessed on 13 September 2022) were used for large-scale analysis and data visualization.
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3

Statistical Analysis of Biological Data

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All analyses were carried out using R statistical platform (https://www.r-project.org) in R-studio version 1.4.1106. Several R-packages were used in data analysis and visualization including readxl, ggplot2, polycor and lares. Fisher’s Exact (FE) test of independence was employed to analyze the associations between nominal variables. Moreover, the correlation between these variables was performed using the Spearman's rank correlation and strength of the association was expressed as Spearman's correlation coefficient (rs) between − 1 and + 1. Kruskal–Wallis (KW) test was used to compare the medians for non-normally distributed quantitative data and Mann–Whitney test was applied as a post-hoc test using Bonferroni correction method for multiple comparisons. For all statistical analyses, p-values ≤ 0.05 were considered statistically significant.
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4

Statistical Analysis of Quantitative Data

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All analyses were carried out using R statistical platform (https://www.r-project.org, accessed on 30 April 2022) in R-studio, version 1.4.1106. In quantitative variables, normality assumption was tested using chi-squared goodness-of-fit test. For normally distributed data, t-test and ANOVA were used to compare the means of two groups and multiple groups, respectively. Kruskal–Wallis (KW) test was used to compare the medians for non-normally distributed data. Mann–Whitney and Tukey’s HSD tests were applied as post hoc tests using Bonferroni correction method for multiple comparisons in the Kruskal–Wallis and ANOVA tests, respectively. For all statistical analyses, p-values < 0.05 were considered statistically significant.
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5

Statistical Analysis of Experimental Data

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All statistical analyses were conducted using the R statistical platform (https://www.r-project.org/) v.3.6.1. Fisher’s exact test and Wilcoxon rank-sum test were used to compare categorical and continuous variables. All statistical tests were two-sided. Benjamini–Hochberg multiple testing correction was applied when appropriate.
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6

Comparative Analysis of Bioactive Compounds

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All experiments were carried out in triplicate, and the data were expressed as the mean ± SD. Statistical analysis was conducted using R statistical platform (https://www.r-project.org (accessed on 30 November 2021)). Among R-packages used in data analysis and visualization are readxl, ggridges and boxplot. Kruskal–Wallis one-way analysis of variance on ranks was used to test the significance among different groups. p-value < 0.05 was considered to indicate statistically significant differences.
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7

Circulating miRNAs for Distinguishing Cardiac Dyspnea

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Continuous variables were expressed as median (interquartile range) and categorical variables as count (percentage). For all analyses, circulating levels of miRNAs were log-transformed. Levels of miRNAs were compared among several group of patients, namely AHF with or without history of CHF (respectively named acute decompensated HF—ADHF—or de novo AHF), acute dyspnea from non-cardiac origin (non-AHF) and stable CHF using first the Kruskal-Wallis test and then the pairwise Wilcoxon test using an adjusted p value according to the Holm method.[23 ]
The ability of miRNAs to discriminate dyspnea of cardiac from non-cardiac origin was studied using receiver operating characteristic (ROC) curve and the area under the ROC curve (AUC).[24 (link), 25 (link)] Association of circulating levels of miRNAs with one-year outcome was assessed using the chi square test. To take into account a potential confounding effect of prognostic covariates, adjusted analyses were performed using logistic regression. The association between miR-423-5p and one-year mortality in the validation cohort was assessed using Kaplan Meier analyses.
Statistical analyses were performed using the R statistical platform (http://www.r-project.org/) and the SigmaPlot v12 software. A 2-sided p value < 0.05 was considered statistically significant.
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8

Investigating Therapeutic Effects in Animal Model

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All data are expressed as mean ± standard error of the mean. Statistical comparisons were performed using one-way ANOVA for parametric tests followed by Dunnett’s test or Kruskal–Wallis of variance for non-parametric tests followed by Steel’s test. Overall and median survival were determined using Kaplan-Meier analyses and log-rank testing of variance. Differences showing values of p < 0.05 were considered statistically significant, as represented by a ‘*’ sign, and p < 0.01 is represented as a ‘**’ sign on the graph. All analyses were performed using the R statistical platform (ver. 3.4.2; https://www.r-project.org/).
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