R version 3

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R version 3.6.1 is a free, open-source software environment for statistical computing and graphics. It is a programming language and software environment for statistical computing and graphics. R version 3.6.1 is the updated version of the R software released in 2019.

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36 protocols using r version 3

Survival Analysis of Hematopoietic Transplant

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Data were locked for analysis on January 23, 2019. Survival endpoint probabilities were estimated using the Kaplan-Meier
method with 95% confidence intervals (CI). Cumulative incidences (CuI) of transplant-related mortality (TRM), GVHD, count
recovery, and graft failure were estimated by competing-risk analysis using Gray’s method. Death was a competing risk for
all analyses except TRM; relapse of pre-BMT malignancy was a competing risk for TRM. Graft failure was a competing risk for
GVHD.
Data were analyzed with R, version 3.3.3 (https://www.R-project.org, R-Foundation for Statistical Computing) and Prism, version 8.0
(GraphPad Software)

Dimitrova D., Gea-Banacloche J., Steinberg S.M., Sadler J.L., Hicks S.N., Carroll E., Wilder J.S., Parta M., Skeffington L., Hughes T.E., Blau J.E., Broadney M.M., Rose J.J., Hsu A.P., Fletcher R., Nunes N.S., Yan X.Y., Telford W.G., Kapoor V., Cohen J.I., Freeman A.F., Garabedian E., Holland S.M., Lisco A., Malech H.L., Notarangelo L.D., Sereti I., Shah N.N., Uzel G., Zerbe C.S., Fowler D.H., Gress R.E., Kanakry C.G, & Kanakry J.A. (2019). Prospective study of a novel, radiation-free, reduced-intensity bone marrow transplantation platform for primary immunodeficiency diseases. Biology of blood and marrow transplantation : journal of the American Society for Blood and Marrow Transplantation, 26(1), 94-106.

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Automated Behavioral Analyses in Mouse Models

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All behaviors were scored using the automated and unbiased Ethovision software. Experimenters analyzing the dataset were blind to the experimental conditions. All mice with an off-target viral injection or fiber implantation were removed from this study (n = 27). The statistic analyses were performed using R (version 3.3.3) and Graphpad (version 8, La Jolla, CA, USA) software. The statistic sample values were analyzed depending on the sample size, normality, and homoscedasticity of the distributions. The normality of the distribution was assessed using Kolmogorov–Smirnov tests. The data fitting assumptions of the general linear model were subjected to linear regression, two-sided student t.tests, or multiple comparisons using a one-way, two-way, or repeated-measures ANOVA followed by post hoc two-sided t-tests with Dunnets and Bonferroni corrected for multiple comparisons t-test p values. Analog non-parametric analyses were performed for datasets that did not follow a normal distribution or homoscedasticity using Spearman correlation analyses, or Kruskal–Wallis and Mann–Whitney two-sided statistical analyses. Statistical significance was set at 0.05.

Morel C., Montgomery S.E., Li L., Durand-de Cuttoli R., Teichman E.M., Juarez B., Tzavaras N., Ku S.M., Flanigan M.E., Cai M., Walsh J.J., Russo S.J., Nestler E.J., Calipari E.S., Friedman A.K, & Han M.H. (2022). Midbrain projection to the basolateral amygdala encodes anxiety-like but not depression-like behaviors. Nature Communications, 13, 1532.

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Sterol and Metabolomic Analyses

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All statistical analyses for sterol data were performed using R version 3.3.3 and Graph Pad Prism v8.0.1. Shapiro–Wilk test was conducted to test for normality. The data was log transformed, if found to be not normal. One-way ANOVA was performed for each sterol, with multiple comparisons by Tukey’s Post Hoc tests. For metabolomics, all data were log transformed and the transformed data were analyzed using MetaboAnalyst v4.0 to generate heat maps, dendrogram clusters, correlation matrix and significance analysis of microarrays plot (SAM plot). Principle component analysis (PCA) plots were generated in MarkerView™ Software v1.2.1.1 (AB SCIEX, Foster City, USA). Means are presented as ± standard errors for means.

Chakrabarti P., Morré J.T., Lucas H.M., Maier C.S, & Sagili R.R. (2019). The omics approach to bee nutritional landscape. Metabolomics, 15(10), 127.

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Metastasis-associated lncRNA Prognostic Signature

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All statistical analyses were conducted with R version 3.4.3 and GraphPad Prism 7.0 software. A volcano plot was drawn using the “ggplot2” package of R software. The associations of continuous and categorical variables were analyzed by the Mann‐Whitney U test and sχ² test, respectively. Differential expressions of lnRNAs between LUAD patients with and without metastasis were analyzed using the edgeR package of R software. Univariate and multivariate Cox analyses were carried out to screen independent prognostic factors of RFS. The Cox regression coefficients were used to establish a prognostic risk formula based on metastasis‐associated lncRNAs. For survival analyses, the Kaplan‐Meier method was used to plot survival curves that were compared by log‐rank tests. Time‐dependent ROC analysis was applied to assess the predictive accuracy of the lncRNA signature. The primary end point was relapse. A value of P < 0.05 was considered statistically significant.

Zhang X., Han J., Du L., Li X., Hao J., Wang L., Zheng G., Duan W., Xie Y., Zhao Y., Zhang X., Zou M, & Wang C. (2020). Unique metastasis‐associated lncRNA signature optimizes prediction of tumor relapse in lung adenocarcinoma. Thoracic Cancer, 11(3), 728-737.

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Prognostic Role of AP-2α in PTC

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All the analyses were completed by R version 3.4.3 or Graphpad prism 5 software, with P <0.05 being considered statistically significant. Data are presented as mean ± SD. Comparisons of continuous variables were made using Student’s t-test. The Mann–Whitney U-test is a nonparametric test used to assess for significant differences in a scale variable by a single dichotomous independent variable. The association between AP-2α mRNA and the clinical pathologic features was analyzed by the Pearson’s chi-squared test or Fisher’s exact test. The Kaplan–Meier method was implemented for the relationship between AP-2α mRNA expression and overall survival (OS) in PTC patients. The cutoff value of AP-2α mRNA expression was determined by its mean value. Cox proportional hazards model was utilized for analysis of prognostic factors.

Wu H.R, & Zhang J. (2018). AP-2α expression in papillary thyroid carcinoma predicts tumor progression and poor prognosis. Cancer Management and Research, 10, 2615-2625.

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Graft Survival Rates in Dialysis Patients

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Graft survival rates were defined as time from biopsy to return to dialysis. Survival functions, censoring for death, were calculated using the Kaplan-Meier method and compared with the Wilcoxon test. Categorical variables were compared using Fisher’s exact test; data for race were compared using the chi-square test. Continuous variables were expressed as mean±SD and analyzed using Student’s t-test. Predictors of graft loss were evaluated using univariate and multivariate Cox proportional hazards models. Variables with p-values <0.1 were selected to construct the multivariate model. All comparisons were two-sided, and p-values <0.05 were considered to be statistically significant. STATA version 13, R version 3.4.3 and GraphPad version 7.0d were used for statistical analysis.

Lan J.H., Gjertson D., Zheng Y., Clark S., Reed E.F, & Cecka J.M. (2018). Clinical Utility of Complement-Dependent C3d Assay in Kidney Recipients Presenting with Late Allograft Dysfunction. American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons, 18(12), 2934-2944.

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Cigarette Smoking Impacts GPR15 Expression

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Associations between cigarette smoking status, GPR15 mRNA expression, and GPR15 DNA methylation were calculated by linear mixed regression models and adjusted for age and sex. Changes in GPR15 gene expression between the baseline and a five-years follow up visit were analyzed by a paired t-test. The threshold for statistical significance was set at p-value (p ≤ 0.05). Bonferroni correction was performed for linear mixed regression models to adjust for multiple testing. Statistical analyses were performed and figures were prepared using the R version 3.4.3 [28 ] and GraphPad prism version 6.05 for Windows (GraphPad Software, La Jolla, CA, USA).

Haase T., Müller C., Krause J., Röthemeier C., Stenzig J., Kunze S., Waldenberger M., Münzel T., Pfeiffer N., Wild P.S., Michal M., Marini F., Karakas M., Lackner K.J., Blankenberg S, & Zeller T. (2018). Novel DNA Methylation Sites Influence GPR15 Expression in Relation to Smoking. Biomolecules, 8(3), 74.

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Rigorous Statistical Analysis Methodology

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Statistical significance of the treatment effects was tested using paired or non-paired Student's t-test depending on the characteristics of the data. Normality and homocedasticity of the data were assessed using Shapiro-Wilkinson and Bartlett or F tests respectively, using the Shapiro.test, Bartlett.test, and var.test functions of R software. Sample size in the animal experiments were calculated employing the sensitivity function of G*Power 3.1 [38] to ensure a power level above 0.95 and a significance level below 0.05. Post-hoc analyses incorporating the actual within and between group variances confirmed a power level above 0.99. Data are expressed as mean±SEM or mean±SD as indicated in figure legends.
Statistical analyses and graphic design were conducted in Prism Software 5 (GraphPad Software Inc.) and R version 3.4.3 (https://www.R-project.org/) [39] . Differences were considered statistically significant when p-value was below 0.05.

Martínez R., Silvan A., Muñoz‐Galdeano T., Reigada D., Águila Á.d., Barreda-Manso M.A., Soto A., & Nieto‐Díaz M. (2020). MicroRNA-138-5p targets pro-apoptotic factors and favours neural cell survival.

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Microbial population analysis protocol

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Where applicable, statistical analysis was performed using either R version 3.5 or GraphPad Prism 8. ANOVA with Tukey’s post hoc analysis was used for parametric analysis of variance between groups, and two-tailed paired Student’s t test or unpaired Welch’s t test was used for pairwise comparisons. The Kruskal-Wallis with Dunn’s test was used for non-parametric analysis of variance between groups, and a two-tailed Wilcoxon rank-sum test or Wilcoxon signed-rank test was used for pairwise comparisons. For longitudinal data analyses, linear mixed effects models were performed using lmerTest (Kuznetsova et al., 2017 ) with multiple testing corrections via the ghlt function of multcomp using TukeyHSD. Analysis and data visualization of microbial populations were carried out in R as described above. Data are presented as mean±SEM unless otherwise noted.

Ang Q.Y., Alexander M., Newman J.C., Tian Y., Cai J., Upadhyay V., Turnbaugh J.A., Verdin E., Hall K.D., Leibel R.L., Ravussin E., Rosenbaum M., Patterson A.D, & Turnbaugh P.J. (2020). Ketogenic diets alter the gut microbiome resulting in decreased intestinal Th17 cells. Cell, 181(6), 1263-1275.e16.

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Evaluating Metabolic Factors in Thyroid Dysfunction

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Data were analysed using R Version 3.5 (20 ) and GraphPad Prism Version 9 (GraphPad, La Jolla, CA). Continuous data are given as mean ± SD unless stated otherwise. TSH values were not normally distributed and log-transformed before further analysis. Simple linear regression was performed for measures of EE and TH levels. In order to correct for potential confounding factors linear modeling was performed as follows: All continuous variables were scaled by Z-scaling. A linear model was built in R containing all anthropometric and laboratory values. Thereafter the model was refined stepwise in order to reduce the number of variables to only significant ones. A p-value below 0.05 was considered significant.

Maushart C.I., Senn J.R., Loeliger R.C., Kraenzlin M.E., Müller J., Becker A.S., Balaz M., Wolfrum C., Burger I.A, & Betz M.J. (2021). Free Thyroxine Levels are Associated with Cold Induced Thermogenesis in Healthy Euthyroid Individuals. Frontiers in Endocrinology, 12, 666595.

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