# Tools for Omics Data Analysis

## Documentation for package ‘POMA’ version 1.20.0

- 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.