Tools for Omics Data Analysis

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Documentation for package ‘POMA’ version 1.19.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

box_cox_transformation	Box-Cox Transformation
cor_pmat	Correlation P-Values
detect_decimals	Detect decimals
flattenCorrMatrix	Flatten Correlation Matrix
PomaBatch	Batch Correction
PomaBoxplots	Boxplots and Violin Plots
PomaClust	Cluster Analysis
PomaCorr	Correlation Analysis
PomaCreateObject	Create a 'SummarizedExperiment' Object
PomaDensity	Density Plots
PomaDESeq	Differential Expression Analysis Based on the Negative Binomial Distribution
PomaEnrichment	Enrichment Analysis
PomaHeatmap	Heatmap Plot
PomaImpute	Impute Missing Values
PomaLasso	Lasso, Ridge, and Elasticnet Regularized Generalized Linear Models for Binary Outcomes
PomaLimma	Differential Expression Analysis Using 'limma'
PomaLM	Linear Models
PomaLMM	Linear Mixed Models
PomaNorm	Normalize Data
PomaOddsRatio	Logistic Regression Model Odds Ratios
PomaOutliers	Analyse and Remove Statistical Outliers
PomaPCA	Principal Components Analysis
PomaPCR	Principal Components Regression
PomaPLS	Partial Least Squares Methods
PomaRandForest	Classification Random Forest
PomaRankProd	Rank Product/Rank Sum Analysis
PomaUMAP	Dimensionality Reduction with UMAP
PomaUnivariate	Univariate Statistical Test
PomaVolcano	Volcano Plot
poma_pal_c	Return function to interpolate a continuous POMA color palette
poma_pal_d	Return function to interpolate a discrete POMA color palette
quantile_norm	Sample Quantile Normalization
scale_color_poma_c	Color scale constructor for continuous 'viridis' "plasma" palette
scale_color_poma_d	Color scale constructor for discrete 'viridis' "plasma" palette
scale_fill_poma_c	Fill scale constructor for continuous 'viridis' "plasma" palette
scale_fill_poma_d	Fill scale constructor for discrete 'viridis' "plasma" palette
st000284	Colorectal Cancer Detection Using Targeted Serum Metabolic Profiling
st000336	Targeted LC/MS of urine from boys with DMD and controls
sum_norm	Sample Sum Normalization
theme_poma	A ggplot theme which allow custom yet consistent styling of plots in the POMA package and web app.