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Table 1 Comparison of Intervene with currently available tools to draw Venn diagrams, UpSet plots and pairwise heatmaps

From: Intervene: a tool for intersection and visualization of multiple gene or genomic region sets

Application

Venn plot types

Upset plot

Pairwise heat map

Weighted venn

Application type

Input type

No. Of inputs

Output type

VennDiagramWeb [12]

Classical Venn, Euler

✘

✘

✘

web app

Lists

5

TIFF, SVG, PNG, R objects

VennPainter [14]

Classical Venn, Edwards, Nested Venn

✘

✘

✘

Stand-alone

Lists

8

SVG, text

Vennture [15]

Edwards

✘

✘

✘

Stand-alone

Lists

6

PowerPoint, Excel

BioVenn [11]

Classical Venn

✘

✘

✓

web app

Lists

3

SVG, PNG

jVenn [13]

Classical Venn, Edwards

✘

✘

✘

web app

Lists

6

PNG and SVG

InteractiVenn [16]

Edwards

✘

✘

✘

web app

Lists

6

SVG, PNG, text

UpSetR [3, 8]

✘

✓

✘

✘

web app, R package

Lists, binary, counts

Multiple

PDF, PNG

ChippeakAnno [5]

Classical Venn

✘

✘

✘

R package

Genomic regions

5

PDF, SVG, PNG

pybedtools [6]

Classical Venn

✘

Matrix only

✓

command line

Genomic regions

3 for Venn, multiple for pairwise

PDF, SVG, PNG

Intervene

Classical Venn, Euler, Edwards, Chow-Ruskey, Square, Battle

✓

✓

✓

command line, web app

Genomic regions, lists, binary, counts

6 for Venn, multiple for upset and pairwise

PDF, SVG, PNG, TIFF, R objects, text