Can any software make the Volcano plot for RNA sequencing data?
I never tried it, but one of these should work.
https://www.rdocumentation.org/packages/a4Base/versions/1.20.0/topics/volcanoPlot
https://www.bioconductor.org/packages/release/bioc/vignettes/EnhancedVolcano/inst/doc/EnhancedVolcano.html
If you're uncomfortable with the technicalities of installation. Just spend some time on it and follow the steps.
Good luck! And feed me back.
TBtools can help do this.
Article TBtools: An Integrative Toolkit Developed for Interactive An...
https://github.com/CJ-Chen/TBtools/releases.
Any software that can create scatter plots can create volcano plots, as volcanoplots are nothing but scatter plots showing -log(P) vs. LFC.
You can use bioinfokit library in python. Here is an example how to use it.
https://reneshbedre.github.io/blog/volcano.html
You can also use orange. It is open-source platform for data visualisation.
https://orange.biolab.si/
1. CLC Genomics Workbench
2. OmicsBox
3. Geneious
Hi! Check the following links and videos.
Good Luck!!
EnhancedVolcano: publication-ready volcano plots with enhanced colouring and labeling
(https://www.bioconductor.org/packages/release/bioc/vignettes/EnhancedVolcano/inst/doc/EnhancedVolcano.html)
Volcano Plots
(https://assets.geneious.com/manual/2020.1/static/GeneiousManualsu110.html)
Volcano plot from multiple t tests
(https://www.graphpad.com/guides/prism/8/statistics/stat_volcano-plot-from-multiple-t-t.htm)
How To Create A Volcano Plot In GraphPad Prism
(https://www.youtube.com/watch?v=oAB3jNspij0)
HDExaminer Featured Feature #6 - The Volcano Plot
(https://www.youtube.com/watch?v=1Ryx-swRPzc)
Instant Clue Tutorial - Volcano Plots
(https://www.youtube.com/watch?v=HmZd5mbFrMU)
Web based platform:
http://45.8.90.25:3838/volcanoR/
The paper:
VolcanoR - web service to produce volcano plots and do basic enrichment analysis
Vladimir Naumov, Ivan Balashov, Vadim Lagutin, Pavel Borovikov, Alexey Alexeevdoi: https://doi.org/10.1101/165100
Good luck
You use DESeq2/EdgeR/Ballgown for RNAseq analysis and related plots ( Volcano plot, MA (mean average) plot, qc-dispersion plots, differential expression heatmaps etc.)
Here are some links:
http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html
https://rnabio.org/module-03-expression/0003/04/01/DE_Visualization/
All the best,
Follow this, it is so easy to understand h
You can use the GraphPad prism software to create a volcano plot. Click on the link below
https://youtu.be/oAB3jNspij0
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