Colleagues, I need help with Venn diagrams and transcriptomics. I have three list of IDs (example: c58516_g4_i4), only IDs, not the sequences. I need to make a Venn diagram, to know which IDs are shared among the three lists, and which only between two of them and which are only present in its original list. I could do it manually, but it's a huge amount of IDs. Can you suggest me some sowtware for windows or script for linux ?. Thanks!
Hi Edgardo,
This will only be helpful if you program in R, but there is a package called "GeneOverlap" that allows you to compare the content of pairs of gene sets (or sets of other types of IDs). To compare the 3 sets with each other, you could compare setA to setB, store the list of commonalities, then compare this list to setC. The final output would be the list of commonalities between all three sets. You can then use the resulting lists and proportions to create a venn diagram using R (package "VennDiagram") or any other program of your choice.
https://www.bioconductor.org/packages/release/bioc/html/GeneOverlap.html
https://cran.r-project.org/web/packages/VennDiagram/VennDiagram.pdf
Hope this helps,
Kristin
Hi Edgardo,
This will only be helpful if you program in R, but there is a package called "GeneOverlap" that allows you to compare the content of pairs of gene sets (or sets of other types of IDs). To compare the 3 sets with each other, you could compare setA to setB, store the list of commonalities, then compare this list to setC. The final output would be the list of commonalities between all three sets. You can then use the resulting lists and proportions to create a venn diagram using R (package "VennDiagram") or any other program of your choice.
https://www.bioconductor.org/packages/release/bioc/html/GeneOverlap.html
https://cran.r-project.org/web/packages/VennDiagram/VennDiagram.pdf
Hope this helps,
Kristin
Simple grepping can be helpful and then venn, but if you want to try a software here is one:
http://bioinformatics.psb.ugent.be/webtools/Venn/
You can try the following tools called "venny". Cheer~
http://bioinfogp.cnb.csic.es/tools/venny/
Take a look at this R-based tool called VennDiagram:
Article Chen H, Boutros PC.. VennDiagram: a package for the generati...
If you are not familiar with R, it is worth learning.
Hello Edgardo, send me an e-mail and I can give you tools to do it!
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