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Table 1 Summary of features implemented by DEvis

From: DEvis: an R package for aggregation and visualization of differential expression data

Feature Class Available Methods
Data Preprocessing TMM Normalization, rlog transform, Variance stabilization,
Replicate merging, P-value / fold change cutoffs, Differential expression
Project Management Standardized project output, Automated data / figure export, High resolution figure generation (pdf / png), Automatic figure size rescaling
Data Manipulation Result set aggregation, Aggregation agreement density plots, P-value filtering, Fold change filtering, Metadata based subsetting, Metadata generation, Metadata modification, Gene ID/name transposition
Clustering Euclidian-based distance, Poisson-based distance, Two-way hierarchical cluster heat mapping, Group-wise dendrograms
Dimensionality Reduction MDS w/ confidence intervals, MDS w/ convex hulls, all genes / differentially expressed only
Distribution Plots Pre-normalization / Post-normalization box plots, Group-wise fold change box plots, Group-wise fold change divergence plots
Expression Plots Up/down regulation summary plots, volcano plots, gene heat maps, gene profile plots
Correlation Plots Group-wise gene expression boxplot w/ Wilcoxon testing, Group-wise gene co-expression plots
Parameter Customization Heat Map/ Profile plot data sorting (max/min/mean/variance/standard deviation), Custom legend/sample labeling, Metadata-based sample grouping, 6 layout/color scheme selections, Visualization data retrieval