Package index

Running the Application

run_app()

Launch the CytokineProfile Shiny App

Exploratory Analysis

Functions for exploring raw data, summarizing statistics, and visualizing key patterns.

cyt_bp()

Boxplots for Continuous Variables with Optional Grouping

cyt_bp2()

Boxplot Function Enhanced for Specific Group Comparisons.

cyt_corr()

Calculate correlations between a target variable and all other numeric variables.

cyt_errbp()

Error-bar Plot

cyt_skku()

Distribution of the Data Set Shown by Skewness and Kurtosis.

cyt_volc()

Volcano Plot.

cyt_heatmap()

Heat Map

cyt_dualflashplot()

Dual-flashlight Plot.

cyt_violin()

Violin Plots for Continuous Variables with Optional Grouping

Univariate Analysis

Functions for performing univariate statistical tests.

cyt_univariate()

Pairwise Univariate Tests Between Two Groups

cyt_univariate_multi()

Univariate Tests for Multi-Level Categorical Predictors

cyt_anova()

ANOVA Analysis on Continuous Variables.

cyt_ttest()

Two Sample T-test Comparisons.

Multivariate Analysis

Functions for deeper multivariate insights.

cyt_splsda()

Analyze data with Sparse Partial Least Squares Discriminant Analysis (sPLS-DA).

cyt_mint_splsda()

Analyze data with MINT Sparse Partial Least Squares Discriminant Analysis (sPLS-DA).

cyt_pca()

Analyze Data with Principal Component Analysis (PCA) for Cytokines.

cyt_plsr()

Perform Partial Least Squares Regression (PLSR) or sparse PLSR (sPLSR) analysis

Machine Learning Methods

cyt_rf()

Run Random Forest Classification on Cytokine Data

cyt_xgb()

Run XGBoost Classification on Cytokine Data

Utility Functions

cyt_export()

Generic export function for Cytokine plots

adjust_p()

Adjust p-values using a specified method

apply_scale()

Apply a scale transformation to numeric columns

Datasets

ExampleData1

Example Cytokine Profiling Data 1.

ExampleData2

Example Cytokine Profiling Data 2.

ExampleData3

Example Cytokine Profiling Data 3.

ExampleData4

Example Cytokine Profiling Data 4.

ExampleData5

Example Cytokine Profiling Data 5.