The largest database of trusted experimental protocols

374 protocols using r statistical software version 3

1

Bacterial Growth and Fungal Dynamics Analysis

Check if the same lab product or an alternative is used in the 5 most similar protocols
Statistical analyses on bacterial growth was performed using R Statistical Software, version 3.6.0 [28 ]. The maximum possible population size in a particular environment, referred to as carrying capacity k, was determined for each growth curve using the R CRAN Packages “growthCurver” [29 (link)]. Carrying capacity k of both strains was compared across the media applying an ANOVA followed by a Tukey post-hoc test.
The analyses of the data collected on white-rot fungi growth was performed using R Statistical Software, version 3.6.0. The R/CRAN Packages used were “tidyverse”, “ggpubr” and “rstatix” [28 ,30 ,31 ,32 (link)]. Data of daily fungal growth rate over time was computed for each fungus by subtracting the previous from the following diametrical measurements and expressed as cm∙day−1. All data firstly underwent the Shapiro–Wilk’s Normality Test. The daily growth rates of the fungi, per each additive and concentrations, were then elaborated by non-parametric Kruskal–Wallis (p < 0.05) to evaluate the presence of significant differences among groups, followed by multiple comparisons between groups using Dunn’s Test (p < 0.05).
+ Open protocol
+ Expand
2

Predicting NAFLD Severity with 3D-MRE and MRI-PDFF

Check if the same lab product or an alternative is used in the 5 most similar protocols
We used the logistic regression model of NAS prediction, including shear stiffness at 60 Hz (coefficient 0.64), damping ratio at 40 Hz (coefficient 0.70), and fat fraction (coefficient 2.46), as previously developed.4 The NAS values predicted by 3D‐MRE/MRI‐PDFF were obtained for each subject at the two time points of interest: bariatric surgery and 1‐year follow‐up. To evaluate the performance of 3D‐MRE combined with MRI‐PDFF to detect changes in NAS (delta NAS = NAS at baseline − NAS at 1 year), we plotted the predicted delta NAS by imaging (y‐axis) compared with the actual delta NAS by histology (x‐axis). Similar plots were obtained for each of the individual components of the model: fat fraction by MRI‐PDFF, shear stiffness at 60 Hz by 3D‐MRE, and damping ratio at 40 Hz by 3D‐MRE. Pearson correlation was used as a statistical measure of performance. The strength of association can be interpreted as small if r < 0.3, moderate if r = 0.3‐0.5, and strong if r > 0.5.
Statistical analyses were performed in SAS v9.4 (SAS Institute, Cary, NC) and R statistical software, version 3.2.0 (R Foundation for Statistical Computing, Vienna, Austria). This prospective study was approved by the Institutional Review Board of the Mayo Clinic.
+ Open protocol
+ Expand
3

Liver Stiffness and PDFF Measurement Comparison

Check if the same lab product or an alternative is used in the 5 most similar protocols
The agreement in liver stiffness and PDFF measurements was evaluated using the coefficient of determination (R2) and Bland-Altman analysis. Measurements were compared between the two readers, and the automated method against each reader. The performance of NASH and NAS score prediction models was evaluated using AUROC and the C-statistic, respectively, in a ten-fold cross validation setup. Statistical analyses were performed in SAS version 9.4 (SAS Institute, Cary, NC) and R statistical software version 3.2.0 (R Foundation for Statistical Computing, Vienna, Austria).
+ Open protocol
+ Expand
4

Comprehensive TCGA Data Analysis Protocol

Check if the same lab product or an alternative is used in the 5 most similar protocols
Data analyses and statistical correlations of TCGA datasets were performed using R Statistical Software version 3.2.0 [81 ] (R Foundation for Statistical Computing, Vienna, Austria). The parameters of beta distributions were estimated by the maximum likelihood estimator implemented in the RPMM package [82 (link)]. Two-sided p values less than 0.05 were considered significant. In order to compare two groups, the non-parametric Mann-Whitney U test was implemented, whereas in case of more than two groups, the Dunn’s multiple comparison test was used. Statistical associations between clinicopathological and molecular factors were determined by Fisher’s exact test using SPSS software version 22.0 (SPSS Inc., Chicago, USA). Survival curves for overall survival (OS) were calculated using the Kaplan-Meier method with log-rank statistics. OS was measured from surgery until death and was censored for patients alive without evidence of death at the last follow-up date. Multivariate Cox regression analysis was performed to test for an independent prognostic value of RBBP8 methylation. Receiver operating characteristics (ROC) curves were calculated to assess biomarker performance of RBBP8 methylation in urine samples [83 (link)].
+ Open protocol
+ Expand
5

Minimally Invasive LVOT Expansion

Check if the same lab product or an alternative is used in the 5 most similar protocols
The sample size of 30 subjects was not statistically derived. Baseline subject and procedural characteristics were summarized as mean ± SD or median and interquartile range for continuous variables and counts and percentages for categorical variables. Wilcoxon signed-rank tests were used to assess the difference in the observed neo-LVOT areas before and after LAMPOON, and the differences in New York Heart Association functional class, 6-min walk distance, and Kansas City Cardiomyopathy Questionnaire quality-of-life summary scores between baseline and 30-day visits. Spearman rank tests assessed relationships between predicted neo-LVOT and skirt neo-LVOT and residual gradients.
Statistical analyses were performed using R statistical software version 3.5.1 (R Foundation for Statistical Computing, Vienna, Austria).
+ Open protocol
+ Expand
6

Statistical Analysis of Global Health Data

Check if the same lab product or an alternative is used in the 5 most similar protocols
Descriptive statistics were used to summarize all demographic variables. Analysis of variance was used to determine statistically significant differences between means for categorical predictors—WHO region and World Bank Income classification. In cases in which significantly different means were identified pairwise t test with Bonferroni correction was used to further delineate statistically significant relationships. All statistical testing was 2-sided and P values less than 0.05 were considered significant. The statistical analysis was conducted using R statistical software, version 3.5.1 (R Foundation for Statistical Computing, Vienna, Austria). Heat matrices were constructed using Tableau Public (Version 2019.3.0) software (Tableau, Seattle, Washington, USA).
+ Open protocol
+ Expand
7

Statistical Software Analyses in Research

Check if the same lab product or an alternative is used in the 5 most similar protocols
All statistical analyses were done using R statistical software version 3.5.1 (R Foundation for Statistical Computing, Vienna, Austria) and SPSS® version 23.0 (IBM, Armonk, New York, USA).
+ Open protocol
+ Expand
8

Analyzing Civic Engagement and Health

Check if the same lab product or an alternative is used in the 5 most similar protocols
We conducted a complete case analysis to test the association between GC participation and self-reported mental and physical health. To account for the nested structure of these data (i.e., by classroom, with students nested within classrooms), we fit linear mixed-effects models. We tested for effect measure modification on the additive scale by including interaction terms in our linear-mixed effects models. The interaction terms, civic self-efficacy and community contributions, were mean-centered to facilitate meaningful interpretation. For the main effects models, statistical significance was assessed at an alpha level of 0.05. As recommended for the purposes of increasing power to detect effect measure modification, statistical significance for the interactions was conservatively assessed at an alpha level of 0.10, recognizing that Selvin suggests an alpha level as high as 0.20 (Selvin, 2004 ). All analyses were conducted in R statistical software version 3.5.1 (R Foundation for Statistical Computing, Vienna, Austria).
+ Open protocol
+ Expand
9

Identifying Human FMR1 Gene Structure

Check if the same lab product or an alternative is used in the 5 most similar protocols
The human genome sequence and the accompanying information pertaining to the gene structure of human FMR1 were obtained from Ensembl version 91 (with genome assembly GRCh38.p10). We developed in-house software to search the sequence pattern including not less than six CGG tandem repeats against the chromosome X sequence. Statistical analysis was conducted using R Statistical Software (version 3.5.1) (R Foundation for Statistical Computing, Vienna, Austria) [54 ]. The FMR1 gene structure was displayed using GSDS 2.0 [55 (link)].
+ Open protocol
+ Expand
10

Logistic Regression for Outcome Prediction

Check if the same lab product or an alternative is used in the 5 most similar protocols
All statistical analyses were performed using the R statistical software, version 3.5.1 (R Foundation for Statistical Computing; statistical https://www.r-project.org/). Logistic regression algorithm, nomogram construction and calibration plots were conducted using the “rms” package. The ROC curve was plotted using the “pROC” package. The Hosmer‐Lemeshow test was performed using the “vcdExtra” package. DCA was performed with the “dca.R” function. All statistical tests were 2‐tailed, and P < 0.05 were considered statistically significant.
+ Open protocol
+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required

Sign up now

Revolutionizing how scientists
search and build protocols!