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
7 answers
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.
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
For this to work, you first have to
- have a tidy data format: A table with columns = variables and rows = observations (genes IDs)
- load your file as .xlsx (using {readxl})
or
- 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.
They won't look like Venn diagrams, but you can visualize overlaps of many different categories with this:
I like InteractiVenn It enables one to save a session so that it is available for quick reference in the future..
Do check there may be duplicate gene ids.
I have used this one in the past. It's great for throwing a quick figure together.
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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.