Tools for Omics Data Analysis


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Documentation for package ‘POMA’ version 1.17.6

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.