Table 1.

Comparison of ResistoXplorer with other web-based tools (except resistomeAnalysis R package) supporting downstream analysis of metagenomic resistome data

Tools	ResistoXplorer	AMR++ Shiny	resistomeAnalysis	WHAM!
Platform	Web-based	Web-based + locally installable	R package	Web-based
Registration	No	No		No
Data processing
Data input	Abundance tables	Abundance tables	Abundance tables	Abundance tables (Biobakery + EBI)
Functional annotation	User-defined + collected from >10 AMR databases	MEGARes	CARD	User-defined
Filtering	Abundance, variance	Abundance (quantile)		Variance
Normalization	Scaling, transformation, rarefying	CSS, rarefying	TSS, proportion	Proportion, clr
Composition profiling
Visual profiling	Stacked bar plot, stacked area, sankey diagram, zoomable sunburst, treemap	Stacked bar plot	Stacked bar plot	Interactive stacked bar plot
Alpha diversity	Multiple		Richness
Ordination analysis	PCoA, NMDS & PCA (2D & 3D)	PCA & NMDS (Bray–Curtis) (2D)	PCoA (2D)
Comparative analysis
Differential analysis	DESeq2, metagenomeSeq, EdgeR, LEfSe, ALDEx2, ANCOM	metagenomeSeq	DESeq2	ALDEx2
Classification	Random Forests, SVM
Other functions	Heatmaps, dendrogram, correlation, core resistome, alpha rarefaction curves	Heatmaps, Alpha rarefaction bar plots	Heatmaps, dendrogram, correlation, core resistome	Interactive Heatmaps, correlation
Integrative analysis	Procrustes, Coinertia, rCCA, sPLS, Spearman, Pearson, CCLasso, MIC		Spearman	Visual comparisons
Gene (ARG) List exploration	ARG-microbial host network visual analytics & functional analysis

ResistoXplorer: http://www.resistoxplorer.no

AMR ++ Shiny: https://github.com/lakinsm/amrplusplus-shiny

resistomeAnalysis (R package): https://github.com/blue-moon22/resistomeAnalysis

WHAM!: https://ruggleslab.shinyapps.io/wham_v1/

Note: Tools exclusively dedicated for sequence annotations are not included.