Searching a venn diagram online tool

Question

[fahim]

Hi

I am searching for a venn diagram online tool to see the similar DGE among two dataset.I know about venny but it does not work for some internet issues.Can any one give me the link of other venny tool by which I can compare themselves. Thanks

[Hamid Ghaedi]

Did you mean venn diagram? if so, please edit your post. Also if you are going to do more and more bioinformatics analysis learning a language like R will help you a lot.

Answer 1

[Papyrus]

I agree with the other comments that taking a programming approach will allow you to do many more things. Nevertheless, regarding online tools, I'm quite fond of this one from the Ghent University (link) because it plots nice intersections for several sets (the 5-set diagram is beautiful), and It will also output you the intersections.

Answer 2

[ponganta]

In R, you could check out {systemPipeR} and systemPipeR::overLapper. It accepts up to seven sets. The package can be used to generate all vennsets (as a list) and even enables visualisation.

Here's some example code. This script assumes that each geneset is a separate file, with gene IDs being newline-separated.

Edit: corrected wrong function name from "vennOverlapper" to "overLapper"

## load libraries

library(systemPipeR)
library(tidyverse)

## load genesets

geneset1 = readLines("path/to/geneset1")
geneset2 = readLines("path/to/geneset2")
geneset3 = readLines("path/to/geneset3")

names_genesets = c("gs1", "gs2", "gs3")

## analyses

setlist = list(geneset1, geneset2, geneset3) %>% setNames(names_genesets)  # list all genesets and name list elements after your genesets

overlaps = overLapper(setlist, type = "vennsets") # generate vennsets

overlaps.ls = overlaps@vennlist # extract vennsets as a list

[fahim]

If my gene set list is in excel sheet,so with that code can i run???

[ponganta]

For this to work, you first have to

1. have a tidy data format: A table with columns = variables and rows = observations (genes IDs)
2. load your file as .xlsx (using {readxl})

or

1. save your tidy .xlsx as a .csv and load the file as .csv-file (comma-separated table)

You would then load the table, extract gene IDs of choice as separate string vectors, and build your venn sets.

[fahim]

The code works but the plot does not shown in R.I also want to draw a plot

[ponganta]

I'd suggest you answer to my answer, not as top-level answer to your post. Check out SystemPipeR's manual. You can use vennPlot() with the generated vennset-object (in my script it's called overlaps).

[fahim]

Oke so how can I visualize this

[Ram]

Please stop adding answers. Use Add Comment or Add Reply instead. I'll be cleaning up your previous posts now, but please be more careful in the future.

Answer 3

[swbarnes2]

They won't look like Venn diagrams, but you can visualize overlaps of many different categories with this:

https://gehlenborglab.shinyapps.io/upsetr/

Answer 4

[Martombo]

If you're like me and you are fond of proportional Venn diagram (or as proportional as possible), you'll enjoy biovenn. It's great to have a visual representation of the overlap among two or three lists.

Answer 5

[Zhilong Jia]

a venn diagram webserver

Answer 6

[Aspire]

I like InteractiVenn It enables one to save a session so that it is available for quick reference in the future..

[fahim]

From my two data set one has 1453 gene and the other has 185,so when i paste my gene into the interactive venn it shows 1309 gene ,instead of showing 1453.But the other gene set number show exactly same.What can be the problem for showing 1309 instead of 1453

[tothepoint]

Do check there may be duplicate gene ids.

Answer 7

[awg]

I have used this one in the past. It's great for throwing a quick figure together.

[Ram]

Please read the question before adding an answer:

I know about venny but it doesnot work for some internet issues