The continuous variables are expressed as mean ± standard deviation, while the categorical variables are expressed as number (%). Group comparisons were performed using one-way analysis of variance and Fisher’s exact test with RStudio software (version 4.0.3). Correlation analysis was performed between the dominant TP and corresponding frequency of maximum hearing threshold using the Spearman rank test. All the statistics and plotting were performed with RStudio software (version 4.0.3). The distribution of TP and frequency of maximum hearing threshold was mapped with Excel. The level of statistical significance was defined as a p-value of <0.05.
Rstudio software
Manufactured by Posit
Sourced in United States, Austria
RStudio is an integrated development environment (IDE) for the R programming language. It provides a user-friendly interface for writing, running, and debugging R scripts. RStudio's core function is to facilitate the development and execution of R code.
Automatically generated - may contain errors
Lab products found in correlation
R software, by R Project for Statistical Computing (6 mentions)
Prism 8, by GraphPad (6 mentions)
Stata 17, by StataCorp (3 mentions)
Prism software, by GraphPad (3 mentions)
Prism 9, by GraphPad (2 mentions)
Spss statistics 23, by IBM (2 mentions)
Spss statistics 26 for windows 10, by IBM (2 mentions)
R software, by Posit (2 mentions)
R version 4, by Posit (2 mentions)
Stata 15, by StataCorp (2 mentions)
Prism 6, by GraphPad (2 mentions)
Prism 7, by GraphPad (2 mentions)
Ultimate 3000 rslcnano system, by Thermo Fisher Scientific (2 mentions)
Prism 8, by Posit (2 mentions)
Sas enterprise guide, by SAS Institute (1 mentions)
Statistical package for the social sciences software, by IBM (1 mentions)
Gmrepo restful apis for r, by R Project for Statistical Computing (1 mentions)
Spss app, by IBM (1 mentions)
Office excel, by Posit (1 mentions)
Jmp pro software, by SAS Institute (1 mentions)
495 protocols using rstudio software
1
Hearing Threshold Frequency Correlation
2
Infant Gut Microbiome Diversity Analysis
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SPSS (v23.0) was used for statistical analysis of infant characteristics, nutrient components of breast milk and clinical data. The α-diversity index analysis (including Shannon and Simpson indices) was performed using QIIME1 (v1.8.0) software. Based on species annotation and relative abundance results, species composition histogram analysis was performed using R Studio software (12 (link)). The beta diversity indices were also calculated using R Studio software. LEfSe (linear discriminant analysis effect size) was used to discover the features contributing to the most variation between control and case groups [LDA (linear discriminant analysis) > 2.0]. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) was used to predict the functional composition of the microbial community metagenome from its 16S profile. The KEGG database was used to obtain KO, pathway and EC information. STAMP (v2.1.3) software package was used for analyzing metabolic profiles (13 (link)).
3
Cervical Intraepithelial Neoplasia Detection Protocol
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Statistical analysis was performed using SPSS software package (SPSS 28, Chicago, IL, USA) and RStudio software (version 1.4.1106). ROC curves were generated based on ∆Ct values to detect CIN2+ and CIN3+ as cut-off, and the AUC was used as a measure of model performance. Kruskal–Wallis test and Mann–Whitney U test were performed to identify differences in methylation levels among two groups or more. Differences in results were considered statistically significant when the p-value was < 0.05. Graphical representations were created with GraphPad Prism 9 or RStudio software (version 1.4.1106).
4
Multivariate Analysis of Neuroimaging Data
5
Interpolation and Detrending for Time Series Analysis
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For the statistical analyses, all records were linearly interpolated to produce evenly spaced time series at intervals of 30 years and subsequently detrended and high-pass–filtered to remove frequencies higher than 1/100 years and thus reduce the noise (fig. S4). Cross-correlations were calculated using the R-Studio software and the package “stats”. The stadial-interstadial tuning points used for the age model were based on change points determined for the original (unsmoothed) records of δ18O in NGRIP and ARM and near-surface temperature in MD99-2284, using the R-Studio software and the “bcp” package (55 ).
6
Statistical Analysis of Experimental Data
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RStudio software (Version 1.2.1335) and GraphPad Prism 8 were used to construct the plots shown in the figures. Statistical analyses were conducted using RStudio software (Version 1.2.1335) and SPSS 22.0 (SPSS, Inc., Chicago, IL, USA). A value of P<0.05 indicated a statistically significant difference.
7
Modeling CAR T-cell Kinetics by IL-15
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A proportional odds logistic regression was used for multivariable modeling of CAR T-cell kinetics according to peak serum IL-15 concentrations in patients treated with CD19 CAR T cells using RStudio software (RStudio, Boston, MA). Other statistical analyses were performed using Prism software (GraphPad, San Diego, CA). Half maximal effective concentration (EC50) values were calculated using 4-parameter nonlinear regression curves. The area under the curve (AUC) was calculated using the trapezoidal rule. Two-tailed Mann-Whitney, unpaired 2-tailed t test, or log-rank tests were used for comparisons. P < .05 was considered statistically significant.
8
Microglial Morphology Analysis via PCA
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Principal component analysis (PCA) was performed in the RStudio Software to further evaluate morphological clustering of microglia using the 13 remaining measured parameters (excluding those used for LDA): NOB, FD, LAC, CP, CHSR, MSACH, CHA, CHP, R, CHC, TRMM, MR and DOB. To select the Principal Components (PCs) that represented the systematic sources of variation in our data and discard PCs that only reflect random noise, a permutation-based test was employed [78 –80 (link)]. PCAtest (https://github.com/arleyc/PCAtest ) was used to evaluate the significance of each PC and of the variable loading for the significant axis [80 (link)]. This function applies a permutation-based test and builds a null distribution to be compared for each parameter [80 (link)]. The cells grouped in the four ROIs identified with the HCA were included in this analysis (243 microglial cells).
9
Microbiome Data Analysis using R Packages
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Statistical analysis and graph processing were conducted on R (Version 4.2.3) using RStudio software (Version 2022.07.0). Several packages were used in the analysis: phyloseq (Version 1.42.0) to facilitate the import, storage, handling and analysis of the microbiome data (McMurdie and Holmes, 2013 (link)), as well as to determine alpha diversity. For the latter, both Chao1 and Shannon indexes were calculated. Vegan (Version 2.6-4) package was used for the permutational multivariate analysis of variance (PERMANOVA) using the Bray Curtis metric distance. The mixOmics package was used for sparse partial least squares discriminant analysis (Rohart et al., 2017 (link)) and the microbiomeMarker (Version 1.4) package for the Linear Discriminant Analysis (LDA) effect size (SE). The ggplot2 (Version 3.4.4) package was used for graphical representation of the data.
10
Survival Analysis of Cancer Patients
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In this study, for all statistical analyses, the R-studio software (version 2022.02.1, https://posit.co/products/open-source/rstudio/ , accessed on 10 March 2022) was employed. The Wilcoxon test was applied to assess differences between normal and tumor groups or between different risk groups. The predictive power of our established signatures was evaluated using ROC (the receiver operating characteristic) curves. Kaplan–Meier survival curves were employed to assess the differences between the survival times of patients in different risk groups.
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