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Table 1 Comparison of BART and leading microarray analysis tools with respect to accepted input, data visualization options, and differential expression/post-processing options

From: BART: bioinformatics array research tool

  Accepted Inputs QC Plots Batch Differential Expression Test Functional Enrich. Analysis
GEO CEL files Expression Table User Table GEO DataSet Volcano Plot PCA Plot Heatmap Box Plots/Bar Graphs
BART Limma KEGG
GEO2R Limma
GEO2Enrichr Characteristic direction or t-test Enrichr
shinyGEO t-test, one gene at a time
GDS Tools Two-tailed or one-tailed t-test, Value means difference, Rank Means Difference FLink